Review Article Molecular Markers and Cotton Genetic Improvement: Current Status...
16
Review Article Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects Waqas Malik, 1 Javaria Ashraf, 1 Muhammad Zaffar Iqbal, 2 Asif Ali Khan, 3 Abdul Qayyum, 1 Muhammad Ali Abid, 1 Etrat Noor, 1 Muhammad Qadir Ahmad, 1 and Ghulam Hasan Abbasi 4 1 Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Pakistan 2 Agricultural Biotechnology Research Institute, Ayub Agriculture Research Institute, Faisalabad, Pakistan 3 Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan 4 University College of Agriculture and Environmental Sciences, e Islamia University of Bahawalpur, Bahawalpur, Pakistan Correspondence should be addressed to Waqas Malik; [email protected] Received 21 July 2014; Accepted 17 September 2014; Published 23 October 2014 Academic Editor: Yeisoo Yu Copyright © 2014 Waqas Malik et al. is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. e availability of draſt genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. e concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. e objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. 1. Introduction Cotton (Gossypium spp.) is considered as the foremost natural fiber and oil source worldwide, with an estimated production and utilization of ∼115 million bales [1]. It is indigenous to tropical and subtropical regions and being cultivated on every continent excluding Antarctica [2]. e economic impact of the cotton industry throughout the world is about ∼$500 billion per year [3]. Despite its economic value, cotton has also an outstanding model system for studying cell elongation, polyploidization, cellulose, and biosynthesis of cell wall [4–6], because it is the only familiar plant that yields single-celled fiber [4]. Cotton belongs to genus Gossypium and family Mal- vaceae. e genus Gossypium has 45 diploid and 5 allote- traploid species and occur in semiarid and arid areas of Africa, Central and South America, Galapagos, Indian sub- continent, Australia, Arabia, and Hawaii [7]. ese 50 species are allotted to 8 diploid genomes (A–G and K) [8–10]. e A, B, E, and F genomes naturally occur in Africa and Asia, while the D genome is indigenous to the America [11]. A third diploid clade, containing C, G, and K, is found in Australia [12]. Currently cotton has only 4 cultivated species, two tetraploid species [G. hirsutum L. (AADD) and G. barbadense L. (AADD), (2 = 4 = 52)] and two dip- loid species [G. arboreum L. (A 2 A 2 ), and G. herbaceum L. Hindawi Publishing Corporation e Scientific World Journal Volume 2014, Article ID 607091, 15 pages http://dx.doi.org/10.1155/2014/607091
Transcript of Review Article Molecular Markers and Cotton Genetic Improvement: Current Status...
Review ArticleMolecular Markers and Cotton Genetic ImprovementCurrent Status and Future Prospects
Waqas Malik1 Javaria Ashraf1 Muhammad Zaffar Iqbal2
Asif Ali Khan3 Abdul Qayyum1 Muhammad Ali Abid1 Etrat Noor1
Muhammad Qadir Ahmad1 and Ghulam Hasan Abbasi4
1 Department of Plant Breeding and Genetics Faculty of Agricultural Sciences and TechnologyBahauddin Zakariya University Multan Pakistan
2 Agricultural Biotechnology Research Institute Ayub Agriculture Research Institute Faisalabad Pakistan3Department of Plant Breeding and Genetics University of Agriculture Faisalabad Pakistan4University College of Agriculture and Environmental Sciences The Islamia University of Bahawalpur Bahawalpur Pakistan
Correspondence should be addressed to Waqas Malik waqasmalikbzuedupk
Received 21 July 2014 Accepted 17 September 2014 Published 23 October 2014
Academic Editor Yeisoo Yu
Copyright copy 2014 Waqas Malik et al This is an open access article distributed under the Creative Commons Attribution Licensewhich permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited
Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L) is stimulating efforts to avail requiredpolymorphism for marker based breeding The availability of draft genome sequence of G raimondii and G arboreum and nextgeneration sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton Theconcepts of genetic diversity QTL mapping and marker assisted selection (MAS) are evolving into more efficient concepts oflinkage disequilibrium association mapping and genomic selection respectively The objective of the current review is to analyzethe pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas (i)comparative analysis of low- and high-throughputmarker technologies available in cotton (ii) genetic diversity in the available wildand improved gene pools of cotton (iii) identification of the genomic regionswithin cotton genome underlying economic traits and(iv) marker based selection methodologies Moreover the applications of marker technologies to enhance the breeding efficiencyin cotton are also summarized Aforementioned genomic technologies and the integration of several other omics resources areexpected to enhance the cotton productivity and meet the global fiber quantity and quality demands
1 Introduction
Cotton (Gossypium spp) is considered as the foremostnatural fiber and oil source worldwide with an estimatedproduction and utilization of sim115 million bales [1] It isindigenous to tropical and subtropical regions and beingcultivated on every continent excluding Antarctica [2] Theeconomic impact of the cotton industry throughout theworldis aboutsim$500 billion per year [3]Despite its economic valuecotton has also an outstanding model system for studyingcell elongation polyploidization cellulose and biosynthesisof cell wall [4ndash6] because it is the only familiar plant thatyields single-celled fiber [4]
Cotton belongs to genus Gossypium and family Mal-vaceae The genus Gossypium has 45 diploid and 5 allote-traploid species and occur in semiarid and arid areas ofAfrica Central and South America Galapagos Indian sub-continent Australia Arabia andHawaii [7]These 50 speciesare allotted to 8 diploid genomes (AndashG and K) [8ndash10] TheA B E and F genomes naturally occur in Africa and Asiawhile the D genome is indigenous to the America [11]A third diploid clade containing C G and K is foundin Australia [12] Currently cotton has only 4 cultivatedspecies two tetraploid species [G hirsutum L (AADD) andG barbadense L (AADD) (2119899 = 4119909 = 52)] and two dip-loid species [G arboreum L (A
2A2) and G herbaceum L
Hindawi Publishing Corporatione Scientific World JournalVolume 2014 Article ID 607091 15 pageshttpdxdoiorg1011552014607091
2 The Scientific World Journal
Table 1 Comparison of marker systems in cotton
Marker Template DNAquantity
Template DNAquality Genetics Cost Reliability Reference
RFLPs High High Codominant High High [26 47 166]RAPDs Low High Dominant Low Low [27 128]ISSRs Low Medium Dominant Low Medium [36 47]SSRs Low Moderate Codominant Low High [27 166]AFLPs Medium Moderate Dominant Moderate High [47 100 128]SNPs Low High Codominant Low High [92 166 167]GBS Low High mdash Low to moderate High [100 168]
(A1A1) (2119899 = 2119909 = 26] [13] Cultivated tetraploid cotton
evolved about 1-2 million years ago through hybridization ofan A genome donor species (G herbaceum and G arboreum)with a D genome (G raimondii and G gossipioides) followedby polyploidization [14ndash16] The progenitor allotetraploidldquoADrdquo diverged and gives rise to ldquoADrdquo tetraploid species (Ghirsutum L and G barbadense L) [17] G hirsutum (Uplandcotton or Mexican cotton) contributes 90 G barbadense(Sea Island cotton or Egyptian cotton) produces 8 [18 19]G herbaceum (Levant cotton) and G arboreum (Tree cotton)together provide 2 of the worldrsquos cotton [20]
Tetraploid genome of cotton is relatively large and con-tains about 2200ndash3000Mb of DNA [21 22] The intraspecificDNA polymorphism is low in this species [23 24] whichmakes it a challenging crop for development of molecularmarkersThere is an undeniable need for highly polymorphicmolecular markers if progress in plant breeding is to be madeusing marker-assisted breeding programs Many extraordi-nary reviews have been written about the different classesof molecular markers used in plants and their applicationin construction of linkage map QTL analysis and marker-assisted selection [25ndash27] The objectives of this review areas follows (i) analysis of the evolution of molecular markertechnologies in cotton genetics (ii) genetic diversity in thewild and cultivated cotton gene pools and (iii) overviewof QTL mapping and marker assisted selection activities incotton
2 Overview of Molecular MarkerTechnologies in Cotton
Molecular markers are the firm landmarks in the genome ofan organism rather than the normal genes because mostlythey do not have the biological impacts and may or maynot relate with phenotypic expression of a trait [26] Thedevelopment of the DNA markers is simple due to theavailability of large scale genomic database [28] In plantbreeding these markers are very helpful in recognitioncharacterization identification of genetic variations markerassisted selection (MAS) linkage mapping and genomicfingerprinting [29] to remove linkage drag in backcrossingand to identify the traits which are not easy to measureby visual observation [30] Molecular marker technologiescan be classified into hybridization based PCR based andsequenced based markers on the basis of their working
mechanism Among these PCR-based markers that israndom amplified polymorphic DNA (RAPD) [23 31 32]amplified fragment length polymorphism (AFLP) [17 33]simple sequence repeats microsatellites (SSRs) [34 35] andinter simple sequence repeats (ISSRs) [36] represent themajor class of markers in cotton genomics due to their highutility and exploitation The comparison of different aspectsof generally used molecular markers is given in Table 1 andbrief description of these three classes of molecular markersis described below with special reference to cotton genetic
21 Hybridization Based DNAMarkers Restriction fragmentlength polymorphism (RFLP) markers reveal the differencesamong individuals by variation in the size of DNA fragmentsproduced by restriction enzymes [27]Thesemarkers enabledDNA variations to be tested as substitutions of a single base inthe recognition sequence of a restriction enzyme altered thelength of resultant restriction fragments [37] In this methodcDNA or synthetic oligonucleotides are used as probes andDNAprofiles are observed by hybridizing the restricted DNAfragment to a labeled probe (labeled with radioisotope)RFLPs can be used to examine the association between theclosely related taxa for study of introgression and gene flowbetween crops and weeds [38] In various species of cottonRFLP markers have been used to study the population genet-ics evolution and phylogenetic relationships [39] Variousreports are published on genetic mapping of cotton usingRFLPs (restriction fragment length polymorphism) [40ndash42]and it was reported that in cotton 64RFLPs are codominantin nature [43] Genetic diversity in upland cotton has alsobeen examined using RFLP markers [38] Molecular map ofthe cotton genome was first constructed using 705 RFLP lociand partitioned into 41 linkage groups [43] The utility ofRFLPmarkers inmarker assisted selection (MAS) is reportedand RFLP linked to resistance allele for pathogen of bacterialblight was validated [44] RFLP markers are very complexand time and cost intensive technique which restricted ituse leading to development of less complicated techniquesknown as PCR base markers [26]
22 PCR BasedMarkers PCR (polymerase chain reaction) isused for replication of small amount of DNA enzymaticallywithout using the living organism DNA polymerase such asTaq polymerase reads and synthesizes a new strand in 51015840-31015840direction using deoxynucleotide triphosphates (dNTPrsquos) It
The Scientific World Journal 3
can not only amplify small quantity of DNA but degradedsources of DNA can also be amplified [45] The reactionof PCR consists of many cycles of denaturation annealingand extension Then the PCR product can be visualizedon agarose or polyacrylamide gels PCR-based technologyhas been utilized widely in analysis of genetic diversity andrecognition of DNA markers Due to the simplicity and highchances of success in PCR many approaches for productionof PCR based molecular markers were described
221 Random Amplified Polymorphic DNA RAPD RAPD isan old PCR based technique that infers DNA polymorphismsdue to deletions or reorganization between the obligatingsites of oligonucleotide primer in the genome [46] InRAPDsDNA fragments are amplified by the PCR reaction usingrandom primers (usually of 10 bp) [47] The sequence ofthe RAPD primers must fulfill the following criteria (i)minimum 40 GC contents and (ii) absence of palindromicsequence [46] A discrete DNA product is produced if thesepriming sites are within an amplifiable range of each other
RAPD techniques have been used for many purposesincluding assessment of genetic variations in population[23 48] DNA fingerprinting [49] and determining therelationship between the genotypes of different and samespecies [50] In cotton RAPDs were used to distinguish thecotton varieties resistant to jassids aphids and mites [51]RAPD marker (R-6592) for the male sterility gene has beenidentified in cotton [52] RAPD techniques are also usedto evaluate the genetic relationship among cotton genotypes[53] to identify the QTLs for stomatal conductance [54] andto construct linkage mapping in cotton
222 Inter Simple Sequence Repeats ISSR In ISSRs DNAfragments are amplified which present between two identicalSSRs directed in contrary directions [47] It allows thedetection of polymorphism in inter SSR loci using primer(16ndash25 bp long) complimentary to a single SSR and annealat either the 31015840 or 51015840 end [47] that can be di tri tetraor pentanucleotide [36] The ISSR primers are commonlyanchored at 31015840 or 51015840 end with 1 to 4 bases stretched into theflanking regions The primers anchored at 31015840 end producemore obvious bands as compared to anchored at 51015840 end [36]The technique of ISSR markers combines many benefits ofAFLPs and SSRs with universality of RAPDs [55] Generallythe sequence of ISSR primers is larger as compare to RAPDprimers allowing higher annealing temperature which out-comes greater reproducibility of bands than RAPDs [36 56]Amplification of ISSRs also revealed larger fragments numberper primer than RAPDs [57] Many earlier studies reportedthat ISSR markers were more informative than RAPDs forgenetic diversity evaluation in different crop species [58 59]
The applications of ISSRs for different purposes dependon the diversity and frequencies of SSR within the particulargenomes [60] It is quickly being utilized by the researchcommunity in different areas of plant improvement that isin gene tagging analysis of genetic diversity and estimationof SSR motif [61ndash63]
223 Amplified Fragment Length Polymorphism AFLPAFLP markers were developed to overcome the problem ofreproducibility connected to RAPDs [64] This techniquedetects large number of loci in a single reaction of PCR [6465] and discovers large number of polymorphism dispersedacross the genome [66] In AFLP assays amplicon numbersare depend on (i) number of selective nucleotides in theprimer (ii) selective nucleotide motif (iii) GC content and(iv) physical genome size [26] AFLP is an effective toolfor the observation of genetic diversity [67] fingerprintingstudies and tagging of agronomic seed and fiber qualitytraits [68ndash70] AFLP is a great valued technique for genemapping studies due to their high abundance and randomdistribution throughout the genome [64] A linkage map ofcotton was developed using the AFLP and RAPD markers[71] AFLP markers have also been used for analyzing thegenetic diversity [17 72] andmap saturation in cotton [19 73]
224 Microsatellites or Simple Sequence Repeats SSR Theseare di- tri- tetra- or pentatandom repeats of nucleotidescattered abundantly in both noncoding and coding regionsof a genome [29 47] Microsatellites are created from spherewhere variants of repetitive DNA sequence are previouslyoverrepresented [74] The loci of these markers are highlytransferable about 50 across species [75] For SSRs analysisforward and reverse primers are employed in PCR reactionthat anneal to the template DNA at the 51015840 and 31015840 ends Shortrepetitive DNA sequences furnish the basis for multi alleliccodominant PCR based molecular marker and found morepolymorphic as compare to other DNA markers [27 47]
Due to their greater polymorphism SSRs are consideredas an important marker system in fingerprinting analysisof genetic diversity molecular mapping and marker assistedselection [76] The availability of SSR markers in the cottongenome make them useful in study of genetic diversity [20]Furthermore over 1000 SSR primers have been designedfrom available cotton DNA sequences in genomic libraries[77] Cotton Gen database is the largest repository for theSSR markers and their mapping information (httpwwwcottongenorgfindmapped markers)
(1) EST-SSRs SSR markers obtained from ESTs (expressedsequence tags) are present in sequences of functional geneand directly associated with transcribed parts of DNA [78]About 1ndash5 of the ESTs in different species of plants haveSSRs of suitable length for development of markers [79] Ascompare to genomic SSRs EST-SSR markers have greaterpotential for transferability between the species [80] EST-SSRs also have a greater possibility of being functionallylinked with variations in gene expression than genomicSSRs [81] Rising number of ESTs for cotton helped in therecognition of SSRs domains from the ESTs by data miningmethods Recently several EST-SSRs have been mappedin cotton [82ndash85] However EST-SSRs exhibit low level ofpolymorphism than conventional SSRs [86]
(2) CAPS Microsatellites Cleaved amplified polymorphicsequence (CAPS) technique is actually the combination of
4 The Scientific World Journal
RFLP and PCR [87] in which DNA fragments are ampli-fied through PCR followed by digestion with a restrictionenzyme [88] Subsequently polymorphisms arise from thevariation in the incidence of restriction sites of identi-fied alleles are detected by gel electrophoresis [88] CAPSmicrosatellite and CAPS are technically alike and use ofmicrosatellite spheres and flanking regions as a templatemay have a decisive improvement over the well-known DNAmarkers in crop species CAPS microsatellites change themonomorphic markers into polymorphic markers whichmostly inherited in codominant way [89] and exhibit highpolymorphism between strongly related genotypes Any basesubstitutions can be identified by CAPS microsatellites as thepolymorphism exhibited by this technique is based on thesequence dissimilarities in the flanking regions aside fromthe microsatellite spheres These markers also assist in theanalysis of composite traits by genemapping and propose theopportunity of identifying markers by physiological and bio-chemical characteristics of their gene products [86]Howeverthe CAPSmarkers are only developedwheremutations createa recognition site for restriction enzyme [87]
23 Sequence Based DNAMarkers
231 Single Nucleotide Polymorphism Variations of singlenucleotide (A T C G) in sequence of individual genomeare known as single nucleotide polymorphism or SNPs [26]These may occur in the noncoding coding and intergenicregions of the genome so allowing the detection of the genesdue to the variations in the sequences of nucleotides [26 90]and these are either nonsynonymous or synonymous withinthe coding regions of the genome Synonymous changes canalter mRNA splicing that result the changes in the phenotypeof an individual [91]
SNP markers are important tool for linkage mappingmap based cloning and marker assisted selection due to thehigh level of polymorphismThe codominant nature of SNPsmakes thesemarkers able to distinguish the heterozygous andhomozygous alleles [92] Narrow genetic base and allotetrap-loid genome has made the discovery of SNPs difficult incotton [93] Recently use of high throughput sequencingtechniques have made it possible to detect great numbersof SNP markers [94 95] including organisms with limitedmolecular studies [96 97] and organisms with slight geneticvariation such as cotton [85] In cotton many researcheshave been conducted to observe diversity characteriza-tion and mapping of SNPs in the nucleotide sequenceof Gossypium genome [98 99] Recently an internationalcollaborative effort has developed 70K SNP chip basedon Illumina Infinium genotyping assay (Unpublished datahttpwwwcottongenorgnode1287616)This high-through-put genotyping assay will be a resource that will be usedglobally by public and private breeders geneticists and otherresearchers to enhance cotton genetic analysis breedinggenome sequence assembly and many other uses SimilarlyGene Chip cotton genome array comprising of 239777 probesets representing 21485 cotton transcripts has been developedand under validation step before commercially available by
Affymetrix (httpwwwaffymetrixcomproducts servicesarraysspecificcottonaffx)The sequences used for SNP chipdevelopment were selected from GenBank dbEST and Ref-Seq contributed by the collaborators globally These high-throughput technologies will be helpful for fine mapping andsubsequent gene discovery for important economic traits incotton Additionally these resources will provide foundationsto initiate genomic selection studies in cotton ultimatelyenhancing genetic gain from breeding
232 Genotyping by Sequencing GBS Genotyping-by-se-quencing (GBS) is a technique that simultaneously detectsand genotypes the SNPs in a genome [100] GBS was devel-oped as a simple but strong access for reducing complexityin complex genomes [101] The development of the GBSlibrary is very simpleThe original GBS method used a singlerestriction enzyme to capture the genomic sequence betweenrestriction sites [101]
The choice of restriction enzyme is a crucial factor inGBS for covering the repetitive regions in the genomesIn the original GBS approach used in maize and barleyone restriction enzyme (RE) ldquoApeKIrdquo was used which ismethylation-sensitive to reduce the complexity of the genomeand to choose hypomethylated sphere of the genome forsequencing [101] A modified GBS approach was also devel-oped in which two enzymes and a Y-adapter were usedto generate ldquouniformrdquo GBS libraries where Adapter 1 andAdapter 2were on opposite ends of every fragment [102] GBSis a multiple approach that can discover thousands of SNPs inan experiment and suitable for population studies genomicselection genetic mapping germplasm characterization andother breeding applications in different organisms [101ndash103]GBS technique can also be employed in species of plants thatdo not have available reference genome In these cases thesequence tags can be deal as dominant markers for analysis[100]
3 Overview of Marker Based CropImprovement Efforts
31 Genetic Diversity in Cotton The success of any breedingprogram mainly depends on the availability of the geneticdiversity in the germplasm resources Understanding of thegenetic relationships among plant genotypes is significantto know the complexity of available germplasm to discoverthe differences in available genotypes and to build up usefulconservation plans [104] Thus evaluation based on themolecular markers can give valuable insight into the geneticstructure of a plant population which helps in the devel-opment of new varieties [105] The genetic diversity studiesin cotton germplasm using different marker technologies aresummarized in Table 2 A narrow genetic base is reported incotton by several workers using different molecular markers[23 38 49 106 107]
RAPD and ISSR techniques have been utilized to analyzegenetic diversity and hybridization and for the incident ofsomaclonal variations in various crops involving cotton [108ndash112] Five prominent studies were conducted to evaluate
The Scientific World Journal 5
Table2Anoverview
ofgenetic
diversity
studies
incotto
nusingmolecular
markers
Marker
Cou
ntry
Popu
latio
ntype
Size
References
RAPD
s
USA
16near-hom
ozygou
selitec
ottongeno
types
80RA
PDprim
ers
[23]
Pakista
n31
Gossypium
species3subspecies
and1interspecifich
ybrid
45RA
PDprim
ers
[115]
USA
10varie
tieso
fUplandcotto
n86
RAPD
prim
ers
[32]
Pakista
n30
cultivarsof
Garboretum
50RA
PDprim
ers
[169]
Iran
13F 1
andF 2
cotto
ngeno
types(Gossypium
hirsutum
)obtainedby
crossin
g30
RAPD
prim
ers
[170]
India
Intraspecific
cotto
nF 1
hybrid
andits
parents
20RA
PDprim
ers
[171]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
40RA
PDprim
ers
[172]
SSRs
USA
24cultivarsof
Ghirsutum
88SSRprim
ers
[173]
China
39accessions
ofG
arboreum
358SSRprim
ers
[174]
China
108accessions
ofAs
iatic
cotto
nand1G
herbaceum
60SSRprim
ers
[175]
China
43sourceso
fUplandcotto
ngerm
plasm
36SSRprim
ers
[124]
France
47geno
typeso
ftetraploidcotto
n320SSRprim
ers
[176]
USA
96accessions
ofG
arboreum
115Genom
icandES
T-SSRs
[177]
Pakistan
8accessions
ofG
hirsutum
32SSRprim
ers
[178]
China
59geno
typeso
fGhirsutum
40ES
T-SSRprim
ers
[179]
Greece
29geno
typeso
fGhirsutum
andan
interspecific
hybrid
12SSRprim
erpairs
[180]
China
56accessions
ofSeaisla
ndcotto
n237SSRprim
ers
[125]
Egypt
28geno
typeso
fEgyptiancotto
n6SSRand5ES
T-SSRprim
er[2]
Pakista
n19
geno
typeso
fBtcotton
104SSRprim
ers
[107]
USA
193cultivarsof
Uplandcotto
n44
8SSRprim
ers
[126]
USA
378accessions
ofG
hirsutum
and3of
Gbarbadense
120SSRprim
ers
[181]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
4SSRprim
ers
[172]
AFL
Ps
USA
11accessions
ofG
hirsutum
and2fro
meach
ofG
arboreum
Gherbaceum
andG
barbadense
4EcoR
I-MseIp
rimersfor
AFL
P[106]
Belgium
Uplandcotto
nwild
species(G
raim
ondiiand
Gthurbrii)
andtheirB
C 3progenies
5AFL
Pprim
ers
[117]
USA
3diploidspecieso
fGossypium
3G
barbadensecultivarsand43
Ghirsutum
accessions
20AFL
Pprim
ers
[13]
USA
29accessions
from
fives
pecies
oftheg
enus
Gossypium
16AFL
Pprim
ers
[17]
India
24lin
esof
Ghirsutum
L6AFL
Pprim
ers
[182]
Norway
131a
ccessio
nsof
Gbarbadan
se8AFL
Pprim
ers
[183]
ISSR
s
Iran
13F 1
andF 2
cotto
ngeno
types(Gossypium
hirsutum
)8ISSR
prim
ers
[170]
Egypt
28Eg
yptia
ncotto
ngeno
types
5ISSR
prim
ers
[2]
India
Intraspecific
cotto
nF 1
hybrid
andits
parents
19ISSR
prim
ers
[171]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
20ISSR
prim
ers
[172]
SNPs
Pakista
n2cultivarsof
tetraploid
cotto
nPrim
ersc
orrespon
dto
FIF1
gene
[184]
USA
24lin
esof
cotto
n270SN
Plociand92
Indel
[99]
6 The Scientific World Journal
genetic diversity using RAPD markers during 90s Geneticdiversity of 16 elite homozygous genotypes obtained fromthe inter-specific hybridization was studied using 80 RAPDmarkers [23] RAPD markers were used to differentiate theG hirsutum lines from the G arboretum [113] Similarly25 short duration genotypes of cotton were analyzed usingarbitrary primers [114] Later [115] studied genetic diversityof 31 Gossypium species 3 subspecies and 1 interspecifichybrid using 45 RAPD primers and the results showed thatgenetic relationship of many species is related to the centerof origin Recently genetic diversity in 18 cotton genotypes ofPakistan studied by 5 RAPD primers showed that two diversegenotypes of cotton (CIM-240 and CIM-443) have resistanceagainst cotton leaf curl virus [116]
AFLP technique was also used to distinguish the dif-ferences among diploid and tetraploid species of cotton byutilizing the variations in ribosomal RNA genes [106] Thegenetic diversity between the upland cotton wild species (Graimondii G thurberii and G sturtianum) and their BC
3
progenies was evaluated usingAFLPmarkers [117] Intra- andinterspecific relatedness of theG barbadense G arboreumGraimondii and G hirsutum are determined by AFLPs whichdemonstrated its usefulness for genetic relatedness acrosswide range of species [17] The relationship between the par-ents and four day neutral backcross generations of cotton wasdetermined using 43 AFLP markers [68] Comparative studywas conducted to evaluate AFLP and RAPD techniques using16 diploid cotton genotypes and it was concluded that AFLPmarkers are more efficient for polymorphism detection andfor analyzing of genetic diversity as compared to RAPDs [72]Similarly genetic diversity of 26 Tanzanian cotton genotypes(Gossypiumhirsutum L) was studied using theAFLPmarkers[66] The results of this study indicated the high values ofgenetic similarity which show the lower genetic diversityamong Tanzanian cotton cultivars Reference [65] mapped98 AFLP markers and assigned 22 distinctive chromoso-mal positions using cytogenetic deletion stocks Mappinginformation enhanced the utilization of AFLPs and can beused to saturate the existing marker frequency over differentchromosomes
In cotton SSRs are considered as a new class of DNAmarkers which hastened cotton genetic diversity and map-ping studies [27] and are important source to observe thetranscribed genes [118] There are multiple reports aboutusing the SSR markers for genetic diversity Reference [119]identified 71 SSR loci with 65 primer pairs and placed themondistinctive chromosomes of cotton Genetic diversity amongUS and Australian cultivars and day neutral lines of Ghirsutum was also analyzed by SSR markers [120]
Further saturation of SSR markers was extended by addi-tion of 204 markers which exhibited 261 segregating bandsgiving rise to 233 mapped loci in cotton [77] Interspecificpolymorphism between G barbadense and G hirsutum wasalso studied using SSR markers and results showed thatpolymorphism between species was high but it was lowwithin species [121] Reference [122] developed new SSRmarkers analyzed the status of 23 chromosomes and foundthat the inter loci distance was 49 cM Diversity among52 different G hirsutum cultivars was studied by 31 SSR
primer pairs and successfully discriminated the 52 cultivarsthrough broader allelic coverage [123] Similarly geneticdiversity of 43 upland cotton varieties [124] 56 sea-islandcotton accessions [125] 19 Bt cotton genotypes [107] 50representative Pakistani genotypes [104] and 193 uplandcotton cultivars [126] were evaluated using 36 237 104 70and 448 SSR markers respectively SSRs have also been usedto assess the genetic purity of the cotton hybrids [127] anddemonstrated as an effective tool for hybrid identification
Recent developments in next generation sequencing(NGS) and RNA-seq technology have generated high-throughput sequence data which facilitated the identificationof SNPs as effective and highly saturated markers for geneticstudies in cotton Genetic variations within and betweenthe different species of cotton have been characterized by1000 SNPs and 279 In-Dels from the 270 and 92 locisegregating in G barbadense and G hirsutum to providemapped molecular markers for crosses within species andintrogression of foreign germplasm in cotton [99] A genomereduction experiment based on the restriction site conserva-tion (GR-RSC) and previously generated assembly of expresssequence tags (ESTs) were used to discover the SNPs in 4accessions of G hirsutum and G barbadense A total 11834and 1679 non-genic and 4327 genic SNPs were identified inthe GR-RSC and EST assemblies using highly conservationparameters The KASPer assays were used to target the 1052(704 nongenic and 348 genic) genome specific SNPs betweenthe G hirsutum accessions [93] The assay then tested forthe Mendelian segregation ratio in the F
2population derived
from a cross of upland cotton (G hirsutum) cultivars
32 QTLs Mapping for Important Economic Traits in Cot-ton The regions in genomes to have genes linked with aquantitative trait are known as quantitative trait loci QTLs[128] and the process of developing linkage maps andperforming QTL analysis is referred to as QTLmapping [129130] QTL analysis stands on the principal of identifying aconnection among phenotype and genotype ofmarkers [128]The QTLs identified in cotton germplasm using differentmarker technologies are summarized in Table 3
RFLPs have been widely used to map genes of economicinterest in cotton Previously RFLP map of G hirsutum andG barbadensewas used tomap 14QTLs for fiber related traits[131] Similarly genes influencing density of stem and leaftrichomes [132] high gossypol plant and low seed gossypolcontents [117] were confined by RFLP markers Reference[131] developed an RFLP map of 261 markers distributedamong 26 linkage groups using F
2plants from an interspecific
cross Another genetic linkage map was developed usingRFLP markers and 26 QTLs were recognized for agronomicand fiber quality traits [41] Later on RFLP based QTLmapping was extended to leaf chlorophyll contents [133]Backcross population of G hirsutum and G barbadense wasused to map 28 9 and 8 QTLs for fiber length lengthuniformity and short fiber contents respectively using the262 RFLP markers [134]
RAPDs have also been widely used for QTL mappingin cotton however lack of reproducibility and unknown
The Scientific World Journal 7
Table3Anoverview
ofQTL
studies
incotto
n
Traits
Descriptor
Popu
latio
nSize
Marker(nu
mbera
ndtype)
QTL
snum
ber
Reference
Fiberq
uality
FSFLandFF
F 2171
RFLP
sand
85RA
PDs
13[135]
FSF 2
186
217SSRs800
RAPD
sUBC
and1040
OPE
RON
2[153]
LYLPSW
NSUQSFFL
FE
FTFFandIF
F 2120
144AFL
PsR
FLPs
and150SSRs
28[14
1]FS
FE
FLFU
LPandFF
F 2117
290SSRs
and9AFL
Ps16
[19]
FFBC
3F2
3662
262RF
LPs
41[185]
FLFLU
andSFC
BC3F
23662
262RF
LPs
45[134]
FSFE
FUFLandFF
RILrsquos
270
7508
SSRs384
SRAPs
and740IT-ISJs
13[186]
FLFSFF
andFE
F 2mdash
1378
SSRs
39[136]
FSFLFFFMTFE
andSFI
RILrsquos
180
4106
SSRsA
FLPsR
APD
sand
SRAPs
48[187]
FEFLFS
FFandFU
CP172
16052SSRs
63[188]
Fibera
ndagrono
mical
SCYLYLPBW
SIFM
TPE
RWFWTFFFLFE
andFS
RILrsquos
188
141S
SRs
56[189]
Yield
andfib
er
FSFLFFFE
LPSINB
SCYandLY
RILrsquos
258
2131
SSRs
53[19
0]
NB
BWSILPLISC
YLYFLFS
FFFE
andFU
4WCandinbred
lines
280
6123
SSRs
andES
T-SSRs
31[138]
SCYLYN
BBW
LPSILIand
FBN
RILrsquos
andIF2
180
2675
EST-SSRs
111
[191]
PHFBN
BWLPLISILYFLFS
FE
FFandFU
Ghirsutum
accessions
81121S
SRs
180
[3]
LISILYSCY
NSB
andFS
F 269
834SSRs437
SRAPs107
RAPD
sand
16RE
MAPs
52[192]
Morph
ological
LBNOSL1L1W1L2
W2L3
andW3
F 2180
261R
FLPs
62[19
3]EM
F 2andF 3
mdash40
83SSRs
54[14
0]NFB
F 2251
1165SSRs
5[19
4]Plant
architectural
PHFBL
FBN
FBA
FBL
PHandNMUB
RILrsquos
180
2130
SSRs2
RAPD
sand
1SRA
P16
[137]
NB
numbero
fbollsperp
lantB
Wb
ollw
eightSIseedindexLP
lintp
ercentL
Ilin
tind
exSIseed
indexSC
Yseed
cotto
nyieldperp
lantLY
linty
ield
perp
lantF
Lfib
erleng
thF
Sfib
erstr
ength
FEfi
ber
elong
ation
FUfiberu
niform
ityratio
FY
fiber
yello
wnessFFfib
erfin
enessFM
Tfib
ermaturityP
Hplant
heightFBL
fruitbranch
leng
thFBN
fruitbranch
numberFB
Afruitbranch
angleFL
Ufiberlength
unifo
rmitySFC
sho
rtfib
ercontentFR
fiberreflectanceSW
seedweightNSnu
mbero
fseeds
perp
lantU
Qupp
erqu
artilelengthSFsho
rtfib
ercontentFT
fibertenacityIFim
maturefi
bercon
tentSFIsho
rtfib
erindexNSB
num
bero
fseeds
perb
ollEM
earlymaturityN
MUB
lowerm
iddleandup
sideb
olln
umberNFB
nod
etofirstfruitin
gbranchLBN
Olob
enum
bersSL1sub
lobe
numbero
nthem
ainlobeL1
main-lobe
leng
thW
1main-lobe
widthL2second
-lobe
leng
thW
2second
-lobe
widthL3third
-lobe
leng
thW
3third
-lobe
leng
thPER
perim
eterW
Fweightfi
tnessWT
wallthicknessFBL
PHratioof
fruit
branch
leng
thto
planth
eightRILrsquosrecom
binant
inbred
linesIF2immortalized
F2s4W
Cfour
way
crossCP
com
positec
rossand
BC3F
2=backcrossfam
ilies
8 The Scientific World Journal
chromosomal positions remained main disadvantages whichrestricted the use of RAPDs in advanced studies Refer-ence [135] used 85 RAPD markers and identified 13 QTLsassociated to the fiber quality in the F
2population derived
from the G hirsutum and G barbadense cross There arenumerous studies on using the RAPDs for QTL mappingalong with other molecular markers (Table 3) An extensiveSSR genotyping was conducted over F
2populations from 3
diverse upland cotton genotypes using 1378 markers and 39fiber related QTLs were identified [136] Recombinant inbredlines (RILs) are also important mapping populations andseveral QTLs related to plant architecture [137] yield [3] andfiber quality [19] have been identified in upland cotton usingRILs About 31QTLs linked to the yield and fiber quality traitsare detected bywide array of SSR and EST SSRmarkers (6123)in 4 way cross populations developed from the 4 inbred linesof G hirsutum [138] A genetic linkage map of the tetraploidcotton was developed using 1601 pairs of SSR and 247 SNPmarkers [139] The genetic map consisted of the 2072 locicovering 3380 cm of the cotton genome Two F
2populations
were generated by the crosses of upland cotton cultivars and4083 SSR markers were used for QTL analysis which detect54 QTLs linked to early maturity [140]
A total of 144 primer combinations of AFLPs and 150 ofSSRs were used to detect 28 QTLs related to the fiber traits[141] To know the significant threshold for the LR statisticspermutation tests were carried out afterwhich 7QTLs remainsignificant RIL lines developed from the intraspecific cross ofupland cotton are used to detect the 12 epistatic and 4 mainQTLs related to the plant architectural traits by 2130 SSR 2RAPD and 1 SRAP markers [137]
Conclusively huge arrays of QTLs have been identifiedusing multiple molecular marker technologies Descriptionof stable QTL from diverse generations common QTL fromvarious populations and homologous QTLs raises the infor-mation on the genetic base Information about distributionof important QTLs in the genome of cotton is very importantand promises the future strategy for marker assisted breed-ing Cotton Gen serves as an important database for suchinformation and currently this database has 988 QTLs for25 different traits (httpwwwcottongenorgdataqtl) whichcan be surveyed according to objectivity
33 Genome Wide Association Studies (GWAS) in CottonAssociation mapping also known as linkage disequilibrium(LD) mapping has appeared as a tool to determine thevariation in complex traits using historical and evolutionaryrecombination actions at the population level [142] In asso-ciation mapping nonstructured populations are phenotypedand genotyped to identify the trait associated with marker[143] This results into capture of wider recombination andhigher resolution mapping as compared to linkage mapping[144] The applications of association mapping for cottonassist extensive employment of natural genetic diversity con-served within the worldwide collections of cotton germplasm[145] as in other plant germplasm resources Turning theefforts of gene-tagging from biparental QTL mapping to LD-based association study promise the productive employment
of ex situ conserved genetic diversity of global germplasmresources of cotton [10] The cotton genome may need fewnumbers of markers for productive associating mappingof complex traits which is also reported for other crops[146] Regarding the tetraploid genome of cotton with atotal recombination length of about 5200 cm and an average400 kb per cm [22] the LD block sizes of sim5-6 cm distanceis sufficient to conduct an association mapping of differenttraits that would require a maximum of sim1000 polymorphicmarkers for successful and reliable associationmapping [147]Extent of genome-wide LD and association mapping offiber quality traits were reported using 95 SSR markers in285 exotic accessions of G hirsutum comprised of 208 lan-draces and 77 varieties [10] Similarly LD-based associationmapping was conducted for fiber quality traits in 335 Ghirsutum germplasm using 202 SSR markers [147] Progressin genome sequencing technology provides an opportunity toproduce large size genotypic data which supports associationmapping over QTL mapping and because of this associationmapping is becoming more common [148]
34 Marker Assisted Selection (MAS) in Cotton Markerassisted selection (MAS) is a procedure by which a phenotypeis selected on the basis of genotype of a marker [128]Selecting the plants in the segregating population that havethe suitable genes combinations is the important componentof plant breeding [149] Once the markers tightly linked tothe genes have been detected breeders may use particularDNA marker to identify the plants carry the genes [150]The effectiveness and cost of MAS are influenced by themarker technique therefore it must be selected carefully[151] During the past two decades RAPDs techniqueshave been used for MAS for getting the glanded plantsand glandless seeds in the interspecific population of Gsturtianum and other species [152] It was exposed that DNAmarkers connected to the major QTL (QTLFS1) for fiberstrength could be utilized inMAS to increase fiber strength ofcommercial varieties in segregating populations [153] SomeRAPD markers were developed into locus specific sequencecharacterized amplified region (SCAR) markers to screen theBC1F4upland cotton For example SCAR 1920marker for the
major fiber strength QTL was developed and has been usedfor selecting desirable genotypes [154] Screening of the SNPswhich aremapped on chromosome 10 recognized extra 3 SNPmarkers thatwere associatedwith blue disease resistance gene(Cbd) which were employed to efficiently characterize a traitallowing MAS for strong levels of blue disease resistance incotton breeding programs [155]
4 Cotton Draft Genome and Its Implication
The increasing information of DNA sequencing allows thediscovery of genes and molecular markers associated withdifferent traits opening new avenues for crop improvement[148] Sequencing of DNA promises to display the spectrumof diversity in the genus Gossypium The tetraploid cottonspecies (2119899 = 4119909 = 52) such as G hirsutum and G bar-
The Scientific World Journal 9
badense are thought to have developed by an allopoly-ploidization that happened nearly 1-2 million years ago inwhich a D-genome species is pollen parent and species of anA-genome is maternal parent [12 156] It is essential to havea basic awareness of the structure of the component genomesto understand the cultivated polyploid genomes their evo-lution and interaction between their subgenomes Towardthe long-term aim of characterizing the diversity amongcotton genomes the cotton geneticists have prioritized the Dgenome progenitor G raimondii for complete sequencing Graimondii has a sim880Mb genome [157] the smallest genomein the genus Gossypium at sim60 of the size of diploid A-genome and 40 of the tetraploids [158] A physical map ofG raimondii genome was assembled and several evidencesreferred that the G raimondii genome is composed of twodifferent qualitative components one that is gene-rich andanother that is repeat-rich [158] About 40976 protein codinggenes and 2355 syntenic blocks identified in the genome ofG raimondii [159] Similarly the sequencing and assemblingof G arboreum genome depicted that 685 of the genomeis covered by repetitive DNA sequences and about 41330protein-coding genes were predicted in the genome of Garboreum [160]
5 Future Prospects
Cotton is a major source of foreign exchange for manycountries around the globe therefore major focus remainsthe enhancement of yield and quality of fiber This challengecan be accomplished by introducing new alleles from wildspecies [161 162] and use of modern molecular technologieshelping in increasing genetic gain of economic traits In thisscenario it is believed that sequencing of the G raimondii[159] and G arboreum [160] draft genomes will facilitate thegene discovery of important traits These genome resourcescan also be used for discovery of high-throughput markerplatforms like Select SNP arrays These high-throughputDNAmarkers will be helpful in recognizing the cotton geno-types carrying desired characters and was successfully usednot only to study the genetic diversity but to develop linkagemaps and mapping agronomic traits [12 20] which arenecessary for acceleration of varietal development Althoughthe QTL mapping for the various traits that is fiber yieldand quality [131] drought tolerance [133] disease resistance[163 164] and pests resistance [165] have been accomplishedin cotton but these may not be helpful to clone causal genesdue to lower marker densities In general the choice of amolecular marker technique is based on reliability statisticalpower and level of polymorphisms Since their inventionthey are being continuously modified for improved utilityto solve many problems and to bring forth automationWhen these markers techniques reach a greater degree ofautomation then it will be suitable to use DNA markersdirecting to a new ldquoGreen Revolutionrdquo in the agriculturalworld
Presently the enormous development of more efficientDNAmarkers will go on in the future because they can serveas an important tool for the plant breeders and geneticists
to develop the cultivars of cotton that are demanded bythe society It has been proposed that SNPs marker willhave large influence on MAS and mapping studies in futuredue to high abundance and development of sophisticateddetection system [195] GBS will clearly become the markergenotyping platform in coming years So the development ofnovel markers such as GBS and SNPs and the accessibility ofmodern technologies such as DNA Chips and microarrayshasten genome mapping and subsequent gene discovery inthe cotton for efficient cotton varietal development
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgment
We are highly thankful to Dr Awais Rasheed (CIMMYTChina) for his valued inputs and comments
References
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[2] K F Abdellatif Y A Khidr Y M Mansy M M Lawendey andY A Soliman ldquoMolecular diversity of Egyptian cotton (Gossyp-ium barbadense L) and its relation to varietal developmentrdquoJournal of Crop Science and Biotechnology vol 15 pp 93ndash992012
[3] T Zhang N Qian X Zhu et al ldquoVariations and transmissionof QTL alleles for yield and fiber qualities in upland cottoncultivars developed in Chinardquo PLoS ONE vol 8 no 2 ArticleID e57220 2013
[4] H J Kim and B A Triplett ldquoCotton fiber growth in plantaand in vitro Models for plant cell elongation and cell wallbiogenesisrdquo Plant Physiology vol 127 no 4 pp 1361ndash1366 2001
[5] Y-L Ruan D J Llewellyn and R T Furbank ldquoSuppressionof sucrose synthase gene expression represses cotton fiber cellinitiation elongation and seed developmentrdquo Plant Cell vol 15no 4 pp 952ndash964 2003
[6] Y-M Qin and Y-X Zhu ldquoHow cotton fibers elongate a tale oflinear cell-growth moderdquo Current Opinion in Plant Biology vol14 no 1 pp 106ndash111 2011
[7] P A Fryxell ldquoA revised taxonomic interpretation of GossypiumL (Malvaceae )rdquo Rheedea vol 2 pp 108ndash165 1992
[8] J O Beasley ldquoThe production of polyploids in gossypiumrdquoJournal of Heredity vol 31 no 1 pp 39ndash48 1940
[9] J E Endrizzi E L Turcotte and R J Kohel ldquoGenetics cytologyand evolution of Gossypiumrdquo Advances in Genetics vol 23 pp271ndash375 1985
[10] I Y Abdurakhmonov R J Kohel J Z Yu et al ldquoMoleculardiversity and associationmapping of fiber quality traits in exoticG hirsutum L germplasmrdquo Genomics vol 92 no 6 pp 478ndash487 2008
[11] J F Wendel and R C Cronn ldquoPolyploidy and the evolutionaryhistory of cottonrdquo Advances in Agronomy vol 78 pp 139ndash1862003
10 The Scientific World Journal
[12] Z J Chen B E Scheffler E Dennis et al ldquoToward sequencingcotton (Gossypium) genomesrdquo Plant Physiology vol 145 no 4pp 1303ndash1310 2007
[13] M J Iqbal O U K Reddy K M El-Zik and A E PepperldquoA genetic bottleneck in the lsquoevolution under domesticationrsquoof upland cotton Gossypium hirsutum L examined using DNAfingerprintingrdquoTheoretical and Applied Genetics vol 103 no 4pp 547ndash554 2001
[14] J O Beasley ldquoThe origin of American tetraploid GossypiumspeciesrdquoThe American Naturalist vol 74 pp 285ndash286 1940
[15] J O Beasley ldquoMeiotic chromosome behavior in species specieshybrids haploids and induced polyploids ofGossypiumrdquoGenet-ics vol 27 no 1 pp 25ndash54 1942
[16] J F Wendel C L Brubaker and A E Percival ldquoGeneticdiversity in Gossypium hirsutum and the origin of uplandcottonrdquoAmerican Journal of Botany vol 79 no 11 pp 1291ndash13101992
[17] A M Abdalla O U K Reddy K M El-Zik and A E PepperldquoGenetic diversity and relationships of diploid and tetraploidcottons revealed using AFLPrdquoTheoretical and Applied Geneticsvol 102 no 2-3 pp 222ndash229 2001
[18] X L Song X Z Sun T Z Zhang and H G Wang ldquoAdvanceson genetic diversity of cotton (Gossypium)rdquo Acta BotanicaBoreali-Occidentalia Sinica vol 24 pp 2393ndash2397 2004
[19] Z-S Zhang Y-H XiaoM Luo et al ldquoConstruction of a geneticlinkage map and QTL analysis of fiber-related traits in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 144 no 1-2 pp91ndash99 2005
[20] H-B Zhang Y Li BWang andPWChee ldquoRecent advances incotton genomicsrdquo International Journal of Plant Genomics vol2008 Article ID 742304 20 pages 2008
[21] K Arumuganathan and E D Earle ldquoNuclear DNA contentof some important plant speciesrdquo Plant Molecular BiologyReporter vol 9 no 3 pp 208ndash218 1991
[22] A H Paterson and R H Smith ldquoFuture horizons biotech-nology of cotton improvementrdquo in Cotton Origin HistoryTechnology and Production pp 415ndash432 John Wiley amp SonsNew York NY USA 1999
[23] V Tatineni R G Cantrell and D D Davis ldquoGenetic diversityin elite cotton germplasm determined by morphological char-acteristics and RAPDsrdquo Crop Science vol 36 no 1 pp 186ndash1921996
[24] C L Brubaker and J F Wendel ldquoRFLP diversity in cottonrdquo inGenetic Improvement of Cotton Emerging Technologies pp 81ndash101 Science Publishers Enfield NH USA 2001
[25] N D Young ldquoConstructing a plant genetic linkage map withDNA markersrdquo in DNA-Based Markers in Plants pp 39ndash57 Kluwer Academic Publishers Dordrecht The Netherlands1994
[26] M Agarwal N Shrivastava andH Padh ldquoAdvances inmolecu-lar marker techniques and their applications in plant sciencesrdquoPlant Cell Reports vol 27 no 4 pp 617ndash631 2008
[27] S Preetha and T S Raveendren ldquoMolecular marker technologyin cottonrdquo Biotechnology and Molecular Biology Reviews vol 3no 2 pp 32ndash45 2008
[28] J R Andersen and T Lubberstedt ldquoFunctional markers inplantsrdquo Trends in Plant Science vol 8 no 11 pp 554ndash560 2003
[29] R K Kalia M K Rai S Kalia R Singh and A K DhawanldquoMicrosatellite markers an overview of the recent progress inplantsrdquo Euphytica vol 177 no 3 pp 309ndash334 2011
[30] N Appleby D Edwards and J Batley ldquoNew technologiesfor ultra-high throughput genotyping in plantsrdquo Methods inMolecular Biology vol 513 pp 19ndash39 2009
[31] Q H Xu X L Zhang and Y C Nie ldquoGenetic diversityevaluation of cultivars (G hirsumtum L) from the Changjiangriver valley and Tellow river valley by RAPD markersrdquo ActaGenetica Sinica vol 28 no 7 pp 683ndash690 2001
[32] H J Lu and G O Myers ldquoGenetic relationships and discrim-ination of ten influential upland cotton varieties using RAPDmarkersrdquoTheoretical and Applied Genetics vol 105 no 2-3 pp325ndash331 2002
[33] I Alvarez and J F Wendel ldquoCryptic interspecific introgressionand genetic differentiation within Gossypium aridum (Mal-vaceae) and its relativesrdquo Evolution vol 60 no 3 pp 505ndash5172006
[34] S Liu RGCantrell J CMcCarty Jr and JM Stewart ldquoSimplesequence repeat-based assessment of genetic diversity in cottonrace stock accessionsrdquoCrop Science vol 40 no 5 pp 1459ndash14692000
[35] L F Zhu X L Zhang and Y C Nie ldquoAnalysis of geneticdiversity in upland cotton (Gossypium hirsutum L) cultivarsfrom China and foreign countries by RAPDs and SSRsrdquo Journalof Agricultural Biotechnology vol 11 pp 450ndash455 2003
[36] M P Reddy N Sarla and E A Siddiq ldquoInter simple sequencerepeat (ISSR) polymorphism and its application in plant breed-ingrdquo Euphytica vol 128 no 1 pp 9ndash17 2002
[37] C Schlotterer ldquoThe evolution of molecular markersmdashjust amatter of fashionrdquo Nature Reviews Genetics vol 5 no 1 pp63ndash69 2004
[38] C L Brubaker and J F Wendel ldquoReevaluating the origin ofdomesticated cotton (Gossypium hirsutum Malvaceae) usingnuclear restriction fragment length polymorphisms (RFLPs)rdquoAmerican Journal of Botany vol 81 no 10 pp 1309ndash1326 1994
[39] Z H Yu Y H Park G R Lazo and R J KohelMolecularMap-ping of the Cotton Genome Agron Abstracts ASA MadisonWis USA 1997
[40] C L Brubaker A H Paterson and J F Wendel ldquoComparativegenetic mapping of allotetraploid cotton and its diploid progen-itorsrdquo Genome vol 42 no 2 pp 184ndash203 1999
[41] M Ulloa and W R Meredith Jr ldquoGenetic linkage map andQTL analysis of agronomic and fiber traits in an intraspecificpopulationrdquo Journal of Cotton Science vol 4 no 3 pp 161ndash1702000
[42] M Ulloa W R Meredith Jr Z W Shappley and A L KahlerldquoRFLP genetic linkage maps from four F
23populations and
a joinmap of Gossypium hirsutum Lrdquo Theoretical and AppliedGenetics vol 104 no 2-3 pp 200ndash208 2002
[43] A J Reinisch J-M Dong C L Brubaker D M Stelly J FWendel and A H Paterson ldquoA detailed RFLP map of cottonGossypium hirsutum x Gossypium barbadense chromosomeorganization and evolution in a disomic polyploid genomerdquoGenetics vol 138 no 3 pp 829ndash847 1994
[44] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoD-subgenome bias of Xcm resistance genes in tetraploidGossypium (cotton) suggests that polyploid formation hascreated novel avenues for evolutionrdquo Genetics vol 149 no 4pp 1987ndash1996 1998
[45] H A Erlich PCR Technology Principles and Applications forDNA Amplification W H Freeman New York NY USA 1991
[46] J G KWilliams A R Kubelik K J Livak J A Rafalski and SV Tingey ldquoDNApolymorphisms amplified by arbitrary primers
The Scientific World Journal 11
are useful as geneticmarkersrdquoNucleic Acids Research vol 18 no22 pp 6531ndash6535 1990
[47] S Khanam A Sham J L Bennetzen and M A M Aly ldquoAnal-ysis of molecular marker-based characterization and geneticvariation in date palm (Phoenix Dactylifera L)rdquo AustralianJournal of Crop Science vol 6 no 8 pp 1236ndash1244 2012
[48] K J Chalmers R Waugh J I Sprent A J Simons and WPowell ldquoDetection of genetic variation between and withinpopulations of Gliricidia sepium and G maculata using RAPDmarkersrdquo Heredity vol 69 pp 465ndash472 1992
[49] D S Multani and B R Lyon ldquoGenetic fingerprinting ofAustralian cotton cultivars with RAPD markersrdquo Genome vol38 no 5 pp 1005ndash1008 1995
[50] M KWajahatullah and J M Stewart ldquoGenomic affinity amongGossypium subgenus Sturtia species by RAPD analysisrdquo inProceeding of the Beltwide Cotton Conference National CottonCouncil p 452 Memphis Tenn USA 1997
[51] C D Geng Z Z Gong J Q Huang and Z C ZhangldquoIdentification of difference between cotton cultivars (G hirsu-tum) using the RAPD methodrdquo Jiangsu Journal of AgriculturalSciences vol 11 no 4 pp 21ndash24 1995
[52] T H Lan C G Cook and A H Paterson ldquoIdentification of aRAPDmarker linked tomale fertility restoration gene in cotton(Gossypium hirsutum L)rdquo Journal of Agricultural Genomics vol1 pp 1ndash5 1999
[53] B Shu K Fenling Z Y Yao Z G Mei Z Q Yuan and W XGang ldquoGenetic diversity analysis of representative elite cottonvarieties in three main cotton regions in China by RAPD andits relation with agronomic characteristicsrdquo Scientia AgriculturaSinica vol 34 pp 597ndash603 2001
[54] M Ulloa R G Cantrell R G Percy E Zeiger and Z Lu ldquoQTLanalysis of stomatal conductance and relationship to lint yieldin an interspecific cottonrdquo Journal of Cotton Science vol 4 no1 pp 10ndash18 2000
[55] B Bornet and M Branchard ldquoNonanchored inter simplesequence repeat (ISSR)markers reproducible and specific toolsfor genome fingerprintingrdquo Plant Molecular Biology Reportervol 19 no 3 pp 209ndash215 2001
[56] T M Culley and A D Wolfe ldquoPopulation genetic structureof the cleistogamous plant species Viola pubescens Aiton (Vio-laceae) as indicated by allozyme and ISSR molecular markersrdquoHeredity vol 86 no 5 pp 545ndash556 2000
[57] J B Wang ldquoISSR markers and their applications in plantgeneticsrdquo Yi Chuan vol 24 no 5 pp 613ndash616 2002
[58] T Nagaoka and Y Ogihara ldquoApplicability of inter-simplesequence repeat polymorphisms inwheat for use asDNAmark-ers in comparison to RFLP and RAPDmarkersrdquoTheoretical andApplied Genetics vol 94 no 5 pp 597ndash602 1997
[59] M Z Galvan B Bornet P A Balatti and M BranchardldquoInter simple sequence repeat (ISSR) markers as a tool for theassessment of both genetic diversity and gene pool origin incommon bean (Phaseolus vulgaris L)rdquo Euphytica vol 132 no3 pp 297ndash301 2003
[60] A Shi S Kantartzi M Mmbaga and P Chen ldquoDevelopmentof ISSR PCR markers for diversity study in dogwood (Cornusspp)rdquo Agriculture and Biology Journal of North America vol 1pp 189ndash194 2010
[61] M W Blair O Panaud and S R McCouch ldquoInter-simplesequence repeat (ISSR) amplification for analysis of microsatel-litemotif frequency and fingerprinting in rice (Oryza sativa L)rdquoTheoretical and Applied Genetics vol 98 no 5 pp 780ndash7921999
[62] B Bornet C Muller F Paulus and M Branchard ldquoHighlyinformative nature of inter simple sequence repeat (ISSR)sequences amplified using tri- and tetra-nucleotide primersfrom DNA of cauliflower (Brassica oleracea var botrytis L)rdquoGenome vol 45 no 5 pp 890ndash896 2002
[63] M Sica G Gamba S Montieri L Gaudio and S AcetoldquoISSR markers show differentiation among Italian populationsofAsparagus acutifolius Lrdquo BMCGenetics vol 6 article 17 2005
[64] P Vos R Hogers M Bleeker et al ldquoAFLP a new technique forDNA fingerprintingrdquo Nucleic Acids Research vol 23 no 21 pp4407ndash4414 1995
[65] G O Myers B Jiang M W Akash A Badigannavar and SSaha ldquoChromosomal assignment of AFLP markers in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 165 no 2 pp391ndash399 2009
[66] K Lukonge L Hersalman and M T Labuschagne ldquoGeneticdiversity of tanzanian cotton revealed by AFLP analysisrdquo inProceedings of the African Crop Science Conference vol 8 pp773ndash776 2007
[67] N Murtaza ldquoCotton genetic diversity study by AFLP markersrdquoElectronic Journal of Biotechnology vol 9 no 4 pp 456ndash4602006
[68] M Zhong J CMcCarty J N Jenkins and S Saha ldquoAssessmentof day-neutral backcross populations of cotton using AFLPmarkersrdquo Journal of Cotton Science vol 6 no 2 pp 97ndash1032002
[69] A Rakshit S Rakshit J Singh et al ldquoAssociation of AFLPand SSR markers with agronomic and fibre quality traits inGossypium hirsutum Lrdquo Journal of Genetics vol 89 no 2 pp155ndash162 2010
[70] A Badigannavar and G Myers ldquoGenetic analysis of AFLPmarkers associated with seed quality traits in upland cotton(Gossypium hirsutum)rdquo in Beltwide Cotton Conferences NewOrleans La USA 2010
[71] M K Altaf J M C D Stewart M K Wajahatullah J Zhangand R G Cantrell ldquoMolecular and morphological geneticsof a trispecies F2 population of cottonrdquo in Proceedings of theBeltwide Cotton Conferences vol 1 pp 448ndash452 New OrleansLa USA January 1997
[72] M K Rana and K V Bhat ldquoA comparison of AFLP andRAPD markers for genetic diversity and cultivar identificationin cottonrdquo Journal of Plant Biochemistry and Biotechnology vol13 no 1 pp 19ndash24 2004
[73] J-M Lacape T-B Nguyen S Thibivilliers et al ldquoA combinedRFLP-SSR-AFLP map of tetraploid cotton based on a Gossyp-ium hirsutum times Gossypium barbadense backcross populationrdquoGenome vol 46 no 4 pp 612ndash626 2003
[74] D TautzM Trick andG A Dover ldquoCryptic simplicity in DNAis amajor source of genetic variationrdquoNature vol 322 no 6080pp 652ndash656 1986
[75] S Saha J Wu J N Jenkins et al ldquoBreeding and genetics effectof chromosome substitutions from Gossypium barbadense L 3-79 into G hirsutum L TM-1 on agronomic and fiber traitsrdquoJournal of Cotton Science vol 8 no 3 pp 162ndash169 2004
[76] O U K Reddy A E Pepper I Abdurakhmonov et al ldquoNewdinucleotide and trinucleotide microsatellite marker resourcesfor cotton genome researchrdquo Journal of Cotton Science vol 5no 2 pp 103ndash113 2001
[77] T B Nguyen M Giband P Brottier A M Risterucci and JM Lascape ldquoWide coverage of the tetraploid cotton genomeusing newly developed microsatellite markersrdquoTheoretical andApplied Genetics vol 109 no 1 pp 167ndash175 2004
12 The Scientific World Journal
[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
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The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
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BioinformaticsAdvances in
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Signal TransductionJournal of
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Evolutionary BiologyInternational Journal of
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Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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International Journal of
Microbiology
2 The Scientific World Journal
Table 1 Comparison of marker systems in cotton
Marker Template DNAquantity
Template DNAquality Genetics Cost Reliability Reference
RFLPs High High Codominant High High [26 47 166]RAPDs Low High Dominant Low Low [27 128]ISSRs Low Medium Dominant Low Medium [36 47]SSRs Low Moderate Codominant Low High [27 166]AFLPs Medium Moderate Dominant Moderate High [47 100 128]SNPs Low High Codominant Low High [92 166 167]GBS Low High mdash Low to moderate High [100 168]
(A1A1) (2119899 = 2119909 = 26] [13] Cultivated tetraploid cotton
evolved about 1-2 million years ago through hybridization ofan A genome donor species (G herbaceum and G arboreum)with a D genome (G raimondii and G gossipioides) followedby polyploidization [14ndash16] The progenitor allotetraploidldquoADrdquo diverged and gives rise to ldquoADrdquo tetraploid species (Ghirsutum L and G barbadense L) [17] G hirsutum (Uplandcotton or Mexican cotton) contributes 90 G barbadense(Sea Island cotton or Egyptian cotton) produces 8 [18 19]G herbaceum (Levant cotton) and G arboreum (Tree cotton)together provide 2 of the worldrsquos cotton [20]
Tetraploid genome of cotton is relatively large and con-tains about 2200ndash3000Mb of DNA [21 22] The intraspecificDNA polymorphism is low in this species [23 24] whichmakes it a challenging crop for development of molecularmarkersThere is an undeniable need for highly polymorphicmolecular markers if progress in plant breeding is to be madeusing marker-assisted breeding programs Many extraordi-nary reviews have been written about the different classesof molecular markers used in plants and their applicationin construction of linkage map QTL analysis and marker-assisted selection [25ndash27] The objectives of this review areas follows (i) analysis of the evolution of molecular markertechnologies in cotton genetics (ii) genetic diversity in thewild and cultivated cotton gene pools and (iii) overviewof QTL mapping and marker assisted selection activities incotton
2 Overview of Molecular MarkerTechnologies in Cotton
Molecular markers are the firm landmarks in the genome ofan organism rather than the normal genes because mostlythey do not have the biological impacts and may or maynot relate with phenotypic expression of a trait [26] Thedevelopment of the DNA markers is simple due to theavailability of large scale genomic database [28] In plantbreeding these markers are very helpful in recognitioncharacterization identification of genetic variations markerassisted selection (MAS) linkage mapping and genomicfingerprinting [29] to remove linkage drag in backcrossingand to identify the traits which are not easy to measureby visual observation [30] Molecular marker technologiescan be classified into hybridization based PCR based andsequenced based markers on the basis of their working
mechanism Among these PCR-based markers that israndom amplified polymorphic DNA (RAPD) [23 31 32]amplified fragment length polymorphism (AFLP) [17 33]simple sequence repeats microsatellites (SSRs) [34 35] andinter simple sequence repeats (ISSRs) [36] represent themajor class of markers in cotton genomics due to their highutility and exploitation The comparison of different aspectsof generally used molecular markers is given in Table 1 andbrief description of these three classes of molecular markersis described below with special reference to cotton genetic
21 Hybridization Based DNAMarkers Restriction fragmentlength polymorphism (RFLP) markers reveal the differencesamong individuals by variation in the size of DNA fragmentsproduced by restriction enzymes [27]Thesemarkers enabledDNA variations to be tested as substitutions of a single base inthe recognition sequence of a restriction enzyme altered thelength of resultant restriction fragments [37] In this methodcDNA or synthetic oligonucleotides are used as probes andDNAprofiles are observed by hybridizing the restricted DNAfragment to a labeled probe (labeled with radioisotope)RFLPs can be used to examine the association between theclosely related taxa for study of introgression and gene flowbetween crops and weeds [38] In various species of cottonRFLP markers have been used to study the population genet-ics evolution and phylogenetic relationships [39] Variousreports are published on genetic mapping of cotton usingRFLPs (restriction fragment length polymorphism) [40ndash42]and it was reported that in cotton 64RFLPs are codominantin nature [43] Genetic diversity in upland cotton has alsobeen examined using RFLP markers [38] Molecular map ofthe cotton genome was first constructed using 705 RFLP lociand partitioned into 41 linkage groups [43] The utility ofRFLPmarkers inmarker assisted selection (MAS) is reportedand RFLP linked to resistance allele for pathogen of bacterialblight was validated [44] RFLP markers are very complexand time and cost intensive technique which restricted ituse leading to development of less complicated techniquesknown as PCR base markers [26]
22 PCR BasedMarkers PCR (polymerase chain reaction) isused for replication of small amount of DNA enzymaticallywithout using the living organism DNA polymerase such asTaq polymerase reads and synthesizes a new strand in 51015840-31015840direction using deoxynucleotide triphosphates (dNTPrsquos) It
The Scientific World Journal 3
can not only amplify small quantity of DNA but degradedsources of DNA can also be amplified [45] The reactionof PCR consists of many cycles of denaturation annealingand extension Then the PCR product can be visualizedon agarose or polyacrylamide gels PCR-based technologyhas been utilized widely in analysis of genetic diversity andrecognition of DNA markers Due to the simplicity and highchances of success in PCR many approaches for productionof PCR based molecular markers were described
221 Random Amplified Polymorphic DNA RAPD RAPD isan old PCR based technique that infers DNA polymorphismsdue to deletions or reorganization between the obligatingsites of oligonucleotide primer in the genome [46] InRAPDsDNA fragments are amplified by the PCR reaction usingrandom primers (usually of 10 bp) [47] The sequence ofthe RAPD primers must fulfill the following criteria (i)minimum 40 GC contents and (ii) absence of palindromicsequence [46] A discrete DNA product is produced if thesepriming sites are within an amplifiable range of each other
RAPD techniques have been used for many purposesincluding assessment of genetic variations in population[23 48] DNA fingerprinting [49] and determining therelationship between the genotypes of different and samespecies [50] In cotton RAPDs were used to distinguish thecotton varieties resistant to jassids aphids and mites [51]RAPD marker (R-6592) for the male sterility gene has beenidentified in cotton [52] RAPD techniques are also usedto evaluate the genetic relationship among cotton genotypes[53] to identify the QTLs for stomatal conductance [54] andto construct linkage mapping in cotton
222 Inter Simple Sequence Repeats ISSR In ISSRs DNAfragments are amplified which present between two identicalSSRs directed in contrary directions [47] It allows thedetection of polymorphism in inter SSR loci using primer(16ndash25 bp long) complimentary to a single SSR and annealat either the 31015840 or 51015840 end [47] that can be di tri tetraor pentanucleotide [36] The ISSR primers are commonlyanchored at 31015840 or 51015840 end with 1 to 4 bases stretched into theflanking regions The primers anchored at 31015840 end producemore obvious bands as compared to anchored at 51015840 end [36]The technique of ISSR markers combines many benefits ofAFLPs and SSRs with universality of RAPDs [55] Generallythe sequence of ISSR primers is larger as compare to RAPDprimers allowing higher annealing temperature which out-comes greater reproducibility of bands than RAPDs [36 56]Amplification of ISSRs also revealed larger fragments numberper primer than RAPDs [57] Many earlier studies reportedthat ISSR markers were more informative than RAPDs forgenetic diversity evaluation in different crop species [58 59]
The applications of ISSRs for different purposes dependon the diversity and frequencies of SSR within the particulargenomes [60] It is quickly being utilized by the researchcommunity in different areas of plant improvement that isin gene tagging analysis of genetic diversity and estimationof SSR motif [61ndash63]
223 Amplified Fragment Length Polymorphism AFLPAFLP markers were developed to overcome the problem ofreproducibility connected to RAPDs [64] This techniquedetects large number of loci in a single reaction of PCR [6465] and discovers large number of polymorphism dispersedacross the genome [66] In AFLP assays amplicon numbersare depend on (i) number of selective nucleotides in theprimer (ii) selective nucleotide motif (iii) GC content and(iv) physical genome size [26] AFLP is an effective toolfor the observation of genetic diversity [67] fingerprintingstudies and tagging of agronomic seed and fiber qualitytraits [68ndash70] AFLP is a great valued technique for genemapping studies due to their high abundance and randomdistribution throughout the genome [64] A linkage map ofcotton was developed using the AFLP and RAPD markers[71] AFLP markers have also been used for analyzing thegenetic diversity [17 72] andmap saturation in cotton [19 73]
224 Microsatellites or Simple Sequence Repeats SSR Theseare di- tri- tetra- or pentatandom repeats of nucleotidescattered abundantly in both noncoding and coding regionsof a genome [29 47] Microsatellites are created from spherewhere variants of repetitive DNA sequence are previouslyoverrepresented [74] The loci of these markers are highlytransferable about 50 across species [75] For SSRs analysisforward and reverse primers are employed in PCR reactionthat anneal to the template DNA at the 51015840 and 31015840 ends Shortrepetitive DNA sequences furnish the basis for multi alleliccodominant PCR based molecular marker and found morepolymorphic as compare to other DNA markers [27 47]
Due to their greater polymorphism SSRs are consideredas an important marker system in fingerprinting analysisof genetic diversity molecular mapping and marker assistedselection [76] The availability of SSR markers in the cottongenome make them useful in study of genetic diversity [20]Furthermore over 1000 SSR primers have been designedfrom available cotton DNA sequences in genomic libraries[77] Cotton Gen database is the largest repository for theSSR markers and their mapping information (httpwwwcottongenorgfindmapped markers)
(1) EST-SSRs SSR markers obtained from ESTs (expressedsequence tags) are present in sequences of functional geneand directly associated with transcribed parts of DNA [78]About 1ndash5 of the ESTs in different species of plants haveSSRs of suitable length for development of markers [79] Ascompare to genomic SSRs EST-SSR markers have greaterpotential for transferability between the species [80] EST-SSRs also have a greater possibility of being functionallylinked with variations in gene expression than genomicSSRs [81] Rising number of ESTs for cotton helped in therecognition of SSRs domains from the ESTs by data miningmethods Recently several EST-SSRs have been mappedin cotton [82ndash85] However EST-SSRs exhibit low level ofpolymorphism than conventional SSRs [86]
(2) CAPS Microsatellites Cleaved amplified polymorphicsequence (CAPS) technique is actually the combination of
4 The Scientific World Journal
RFLP and PCR [87] in which DNA fragments are ampli-fied through PCR followed by digestion with a restrictionenzyme [88] Subsequently polymorphisms arise from thevariation in the incidence of restriction sites of identi-fied alleles are detected by gel electrophoresis [88] CAPSmicrosatellite and CAPS are technically alike and use ofmicrosatellite spheres and flanking regions as a templatemay have a decisive improvement over the well-known DNAmarkers in crop species CAPS microsatellites change themonomorphic markers into polymorphic markers whichmostly inherited in codominant way [89] and exhibit highpolymorphism between strongly related genotypes Any basesubstitutions can be identified by CAPS microsatellites as thepolymorphism exhibited by this technique is based on thesequence dissimilarities in the flanking regions aside fromthe microsatellite spheres These markers also assist in theanalysis of composite traits by genemapping and propose theopportunity of identifying markers by physiological and bio-chemical characteristics of their gene products [86]Howeverthe CAPSmarkers are only developedwheremutations createa recognition site for restriction enzyme [87]
23 Sequence Based DNAMarkers
231 Single Nucleotide Polymorphism Variations of singlenucleotide (A T C G) in sequence of individual genomeare known as single nucleotide polymorphism or SNPs [26]These may occur in the noncoding coding and intergenicregions of the genome so allowing the detection of the genesdue to the variations in the sequences of nucleotides [26 90]and these are either nonsynonymous or synonymous withinthe coding regions of the genome Synonymous changes canalter mRNA splicing that result the changes in the phenotypeof an individual [91]
SNP markers are important tool for linkage mappingmap based cloning and marker assisted selection due to thehigh level of polymorphismThe codominant nature of SNPsmakes thesemarkers able to distinguish the heterozygous andhomozygous alleles [92] Narrow genetic base and allotetrap-loid genome has made the discovery of SNPs difficult incotton [93] Recently use of high throughput sequencingtechniques have made it possible to detect great numbersof SNP markers [94 95] including organisms with limitedmolecular studies [96 97] and organisms with slight geneticvariation such as cotton [85] In cotton many researcheshave been conducted to observe diversity characteriza-tion and mapping of SNPs in the nucleotide sequenceof Gossypium genome [98 99] Recently an internationalcollaborative effort has developed 70K SNP chip basedon Illumina Infinium genotyping assay (Unpublished datahttpwwwcottongenorgnode1287616)This high-through-put genotyping assay will be a resource that will be usedglobally by public and private breeders geneticists and otherresearchers to enhance cotton genetic analysis breedinggenome sequence assembly and many other uses SimilarlyGene Chip cotton genome array comprising of 239777 probesets representing 21485 cotton transcripts has been developedand under validation step before commercially available by
Affymetrix (httpwwwaffymetrixcomproducts servicesarraysspecificcottonaffx)The sequences used for SNP chipdevelopment were selected from GenBank dbEST and Ref-Seq contributed by the collaborators globally These high-throughput technologies will be helpful for fine mapping andsubsequent gene discovery for important economic traits incotton Additionally these resources will provide foundationsto initiate genomic selection studies in cotton ultimatelyenhancing genetic gain from breeding
232 Genotyping by Sequencing GBS Genotyping-by-se-quencing (GBS) is a technique that simultaneously detectsand genotypes the SNPs in a genome [100] GBS was devel-oped as a simple but strong access for reducing complexityin complex genomes [101] The development of the GBSlibrary is very simpleThe original GBS method used a singlerestriction enzyme to capture the genomic sequence betweenrestriction sites [101]
The choice of restriction enzyme is a crucial factor inGBS for covering the repetitive regions in the genomesIn the original GBS approach used in maize and barleyone restriction enzyme (RE) ldquoApeKIrdquo was used which ismethylation-sensitive to reduce the complexity of the genomeand to choose hypomethylated sphere of the genome forsequencing [101] A modified GBS approach was also devel-oped in which two enzymes and a Y-adapter were usedto generate ldquouniformrdquo GBS libraries where Adapter 1 andAdapter 2were on opposite ends of every fragment [102] GBSis a multiple approach that can discover thousands of SNPs inan experiment and suitable for population studies genomicselection genetic mapping germplasm characterization andother breeding applications in different organisms [101ndash103]GBS technique can also be employed in species of plants thatdo not have available reference genome In these cases thesequence tags can be deal as dominant markers for analysis[100]
3 Overview of Marker Based CropImprovement Efforts
31 Genetic Diversity in Cotton The success of any breedingprogram mainly depends on the availability of the geneticdiversity in the germplasm resources Understanding of thegenetic relationships among plant genotypes is significantto know the complexity of available germplasm to discoverthe differences in available genotypes and to build up usefulconservation plans [104] Thus evaluation based on themolecular markers can give valuable insight into the geneticstructure of a plant population which helps in the devel-opment of new varieties [105] The genetic diversity studiesin cotton germplasm using different marker technologies aresummarized in Table 2 A narrow genetic base is reported incotton by several workers using different molecular markers[23 38 49 106 107]
RAPD and ISSR techniques have been utilized to analyzegenetic diversity and hybridization and for the incident ofsomaclonal variations in various crops involving cotton [108ndash112] Five prominent studies were conducted to evaluate
The Scientific World Journal 5
Table2Anoverview
ofgenetic
diversity
studies
incotto
nusingmolecular
markers
Marker
Cou
ntry
Popu
latio
ntype
Size
References
RAPD
s
USA
16near-hom
ozygou
selitec
ottongeno
types
80RA
PDprim
ers
[23]
Pakista
n31
Gossypium
species3subspecies
and1interspecifich
ybrid
45RA
PDprim
ers
[115]
USA
10varie
tieso
fUplandcotto
n86
RAPD
prim
ers
[32]
Pakista
n30
cultivarsof
Garboretum
50RA
PDprim
ers
[169]
Iran
13F 1
andF 2
cotto
ngeno
types(Gossypium
hirsutum
)obtainedby
crossin
g30
RAPD
prim
ers
[170]
India
Intraspecific
cotto
nF 1
hybrid
andits
parents
20RA
PDprim
ers
[171]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
40RA
PDprim
ers
[172]
SSRs
USA
24cultivarsof
Ghirsutum
88SSRprim
ers
[173]
China
39accessions
ofG
arboreum
358SSRprim
ers
[174]
China
108accessions
ofAs
iatic
cotto
nand1G
herbaceum
60SSRprim
ers
[175]
China
43sourceso
fUplandcotto
ngerm
plasm
36SSRprim
ers
[124]
France
47geno
typeso
ftetraploidcotto
n320SSRprim
ers
[176]
USA
96accessions
ofG
arboreum
115Genom
icandES
T-SSRs
[177]
Pakistan
8accessions
ofG
hirsutum
32SSRprim
ers
[178]
China
59geno
typeso
fGhirsutum
40ES
T-SSRprim
ers
[179]
Greece
29geno
typeso
fGhirsutum
andan
interspecific
hybrid
12SSRprim
erpairs
[180]
China
56accessions
ofSeaisla
ndcotto
n237SSRprim
ers
[125]
Egypt
28geno
typeso
fEgyptiancotto
n6SSRand5ES
T-SSRprim
er[2]
Pakista
n19
geno
typeso
fBtcotton
104SSRprim
ers
[107]
USA
193cultivarsof
Uplandcotto
n44
8SSRprim
ers
[126]
USA
378accessions
ofG
hirsutum
and3of
Gbarbadense
120SSRprim
ers
[181]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
4SSRprim
ers
[172]
AFL
Ps
USA
11accessions
ofG
hirsutum
and2fro
meach
ofG
arboreum
Gherbaceum
andG
barbadense
4EcoR
I-MseIp
rimersfor
AFL
P[106]
Belgium
Uplandcotto
nwild
species(G
raim
ondiiand
Gthurbrii)
andtheirB
C 3progenies
5AFL
Pprim
ers
[117]
USA
3diploidspecieso
fGossypium
3G
barbadensecultivarsand43
Ghirsutum
accessions
20AFL
Pprim
ers
[13]
USA
29accessions
from
fives
pecies
oftheg
enus
Gossypium
16AFL
Pprim
ers
[17]
India
24lin
esof
Ghirsutum
L6AFL
Pprim
ers
[182]
Norway
131a
ccessio
nsof
Gbarbadan
se8AFL
Pprim
ers
[183]
ISSR
s
Iran
13F 1
andF 2
cotto
ngeno
types(Gossypium
hirsutum
)8ISSR
prim
ers
[170]
Egypt
28Eg
yptia
ncotto
ngeno
types
5ISSR
prim
ers
[2]
India
Intraspecific
cotto
nF 1
hybrid
andits
parents
19ISSR
prim
ers
[171]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
20ISSR
prim
ers
[172]
SNPs
Pakista
n2cultivarsof
tetraploid
cotto
nPrim
ersc
orrespon
dto
FIF1
gene
[184]
USA
24lin
esof
cotto
n270SN
Plociand92
Indel
[99]
6 The Scientific World Journal
genetic diversity using RAPD markers during 90s Geneticdiversity of 16 elite homozygous genotypes obtained fromthe inter-specific hybridization was studied using 80 RAPDmarkers [23] RAPD markers were used to differentiate theG hirsutum lines from the G arboretum [113] Similarly25 short duration genotypes of cotton were analyzed usingarbitrary primers [114] Later [115] studied genetic diversityof 31 Gossypium species 3 subspecies and 1 interspecifichybrid using 45 RAPD primers and the results showed thatgenetic relationship of many species is related to the centerof origin Recently genetic diversity in 18 cotton genotypes ofPakistan studied by 5 RAPD primers showed that two diversegenotypes of cotton (CIM-240 and CIM-443) have resistanceagainst cotton leaf curl virus [116]
AFLP technique was also used to distinguish the dif-ferences among diploid and tetraploid species of cotton byutilizing the variations in ribosomal RNA genes [106] Thegenetic diversity between the upland cotton wild species (Graimondii G thurberii and G sturtianum) and their BC
3
progenies was evaluated usingAFLPmarkers [117] Intra- andinterspecific relatedness of theG barbadense G arboreumGraimondii and G hirsutum are determined by AFLPs whichdemonstrated its usefulness for genetic relatedness acrosswide range of species [17] The relationship between the par-ents and four day neutral backcross generations of cotton wasdetermined using 43 AFLP markers [68] Comparative studywas conducted to evaluate AFLP and RAPD techniques using16 diploid cotton genotypes and it was concluded that AFLPmarkers are more efficient for polymorphism detection andfor analyzing of genetic diversity as compared to RAPDs [72]Similarly genetic diversity of 26 Tanzanian cotton genotypes(Gossypiumhirsutum L) was studied using theAFLPmarkers[66] The results of this study indicated the high values ofgenetic similarity which show the lower genetic diversityamong Tanzanian cotton cultivars Reference [65] mapped98 AFLP markers and assigned 22 distinctive chromoso-mal positions using cytogenetic deletion stocks Mappinginformation enhanced the utilization of AFLPs and can beused to saturate the existing marker frequency over differentchromosomes
In cotton SSRs are considered as a new class of DNAmarkers which hastened cotton genetic diversity and map-ping studies [27] and are important source to observe thetranscribed genes [118] There are multiple reports aboutusing the SSR markers for genetic diversity Reference [119]identified 71 SSR loci with 65 primer pairs and placed themondistinctive chromosomes of cotton Genetic diversity amongUS and Australian cultivars and day neutral lines of Ghirsutum was also analyzed by SSR markers [120]
Further saturation of SSR markers was extended by addi-tion of 204 markers which exhibited 261 segregating bandsgiving rise to 233 mapped loci in cotton [77] Interspecificpolymorphism between G barbadense and G hirsutum wasalso studied using SSR markers and results showed thatpolymorphism between species was high but it was lowwithin species [121] Reference [122] developed new SSRmarkers analyzed the status of 23 chromosomes and foundthat the inter loci distance was 49 cM Diversity among52 different G hirsutum cultivars was studied by 31 SSR
primer pairs and successfully discriminated the 52 cultivarsthrough broader allelic coverage [123] Similarly geneticdiversity of 43 upland cotton varieties [124] 56 sea-islandcotton accessions [125] 19 Bt cotton genotypes [107] 50representative Pakistani genotypes [104] and 193 uplandcotton cultivars [126] were evaluated using 36 237 104 70and 448 SSR markers respectively SSRs have also been usedto assess the genetic purity of the cotton hybrids [127] anddemonstrated as an effective tool for hybrid identification
Recent developments in next generation sequencing(NGS) and RNA-seq technology have generated high-throughput sequence data which facilitated the identificationof SNPs as effective and highly saturated markers for geneticstudies in cotton Genetic variations within and betweenthe different species of cotton have been characterized by1000 SNPs and 279 In-Dels from the 270 and 92 locisegregating in G barbadense and G hirsutum to providemapped molecular markers for crosses within species andintrogression of foreign germplasm in cotton [99] A genomereduction experiment based on the restriction site conserva-tion (GR-RSC) and previously generated assembly of expresssequence tags (ESTs) were used to discover the SNPs in 4accessions of G hirsutum and G barbadense A total 11834and 1679 non-genic and 4327 genic SNPs were identified inthe GR-RSC and EST assemblies using highly conservationparameters The KASPer assays were used to target the 1052(704 nongenic and 348 genic) genome specific SNPs betweenthe G hirsutum accessions [93] The assay then tested forthe Mendelian segregation ratio in the F
2population derived
from a cross of upland cotton (G hirsutum) cultivars
32 QTLs Mapping for Important Economic Traits in Cot-ton The regions in genomes to have genes linked with aquantitative trait are known as quantitative trait loci QTLs[128] and the process of developing linkage maps andperforming QTL analysis is referred to as QTLmapping [129130] QTL analysis stands on the principal of identifying aconnection among phenotype and genotype ofmarkers [128]The QTLs identified in cotton germplasm using differentmarker technologies are summarized in Table 3
RFLPs have been widely used to map genes of economicinterest in cotton Previously RFLP map of G hirsutum andG barbadensewas used tomap 14QTLs for fiber related traits[131] Similarly genes influencing density of stem and leaftrichomes [132] high gossypol plant and low seed gossypolcontents [117] were confined by RFLP markers Reference[131] developed an RFLP map of 261 markers distributedamong 26 linkage groups using F
2plants from an interspecific
cross Another genetic linkage map was developed usingRFLP markers and 26 QTLs were recognized for agronomicand fiber quality traits [41] Later on RFLP based QTLmapping was extended to leaf chlorophyll contents [133]Backcross population of G hirsutum and G barbadense wasused to map 28 9 and 8 QTLs for fiber length lengthuniformity and short fiber contents respectively using the262 RFLP markers [134]
RAPDs have also been widely used for QTL mappingin cotton however lack of reproducibility and unknown
The Scientific World Journal 7
Table3Anoverview
ofQTL
studies
incotto
n
Traits
Descriptor
Popu
latio
nSize
Marker(nu
mbera
ndtype)
QTL
snum
ber
Reference
Fiberq
uality
FSFLandFF
F 2171
RFLP
sand
85RA
PDs
13[135]
FSF 2
186
217SSRs800
RAPD
sUBC
and1040
OPE
RON
2[153]
LYLPSW
NSUQSFFL
FE
FTFFandIF
F 2120
144AFL
PsR
FLPs
and150SSRs
28[14
1]FS
FE
FLFU
LPandFF
F 2117
290SSRs
and9AFL
Ps16
[19]
FFBC
3F2
3662
262RF
LPs
41[185]
FLFLU
andSFC
BC3F
23662
262RF
LPs
45[134]
FSFE
FUFLandFF
RILrsquos
270
7508
SSRs384
SRAPs
and740IT-ISJs
13[186]
FLFSFF
andFE
F 2mdash
1378
SSRs
39[136]
FSFLFFFMTFE
andSFI
RILrsquos
180
4106
SSRsA
FLPsR
APD
sand
SRAPs
48[187]
FEFLFS
FFandFU
CP172
16052SSRs
63[188]
Fibera
ndagrono
mical
SCYLYLPBW
SIFM
TPE
RWFWTFFFLFE
andFS
RILrsquos
188
141S
SRs
56[189]
Yield
andfib
er
FSFLFFFE
LPSINB
SCYandLY
RILrsquos
258
2131
SSRs
53[19
0]
NB
BWSILPLISC
YLYFLFS
FFFE
andFU
4WCandinbred
lines
280
6123
SSRs
andES
T-SSRs
31[138]
SCYLYN
BBW
LPSILIand
FBN
RILrsquos
andIF2
180
2675
EST-SSRs
111
[191]
PHFBN
BWLPLISILYFLFS
FE
FFandFU
Ghirsutum
accessions
81121S
SRs
180
[3]
LISILYSCY
NSB
andFS
F 269
834SSRs437
SRAPs107
RAPD
sand
16RE
MAPs
52[192]
Morph
ological
LBNOSL1L1W1L2
W2L3
andW3
F 2180
261R
FLPs
62[19
3]EM
F 2andF 3
mdash40
83SSRs
54[14
0]NFB
F 2251
1165SSRs
5[19
4]Plant
architectural
PHFBL
FBN
FBA
FBL
PHandNMUB
RILrsquos
180
2130
SSRs2
RAPD
sand
1SRA
P16
[137]
NB
numbero
fbollsperp
lantB
Wb
ollw
eightSIseedindexLP
lintp
ercentL
Ilin
tind
exSIseed
indexSC
Yseed
cotto
nyieldperp
lantLY
linty
ield
perp
lantF
Lfib
erleng
thF
Sfib
erstr
ength
FEfi
ber
elong
ation
FUfiberu
niform
ityratio
FY
fiber
yello
wnessFFfib
erfin
enessFM
Tfib
ermaturityP
Hplant
heightFBL
fruitbranch
leng
thFBN
fruitbranch
numberFB
Afruitbranch
angleFL
Ufiberlength
unifo
rmitySFC
sho
rtfib
ercontentFR
fiberreflectanceSW
seedweightNSnu
mbero
fseeds
perp
lantU
Qupp
erqu
artilelengthSFsho
rtfib
ercontentFT
fibertenacityIFim
maturefi
bercon
tentSFIsho
rtfib
erindexNSB
num
bero
fseeds
perb
ollEM
earlymaturityN
MUB
lowerm
iddleandup
sideb
olln
umberNFB
nod
etofirstfruitin
gbranchLBN
Olob
enum
bersSL1sub
lobe
numbero
nthem
ainlobeL1
main-lobe
leng
thW
1main-lobe
widthL2second
-lobe
leng
thW
2second
-lobe
widthL3third
-lobe
leng
thW
3third
-lobe
leng
thPER
perim
eterW
Fweightfi
tnessWT
wallthicknessFBL
PHratioof
fruit
branch
leng
thto
planth
eightRILrsquosrecom
binant
inbred
linesIF2immortalized
F2s4W
Cfour
way
crossCP
com
positec
rossand
BC3F
2=backcrossfam
ilies
8 The Scientific World Journal
chromosomal positions remained main disadvantages whichrestricted the use of RAPDs in advanced studies Refer-ence [135] used 85 RAPD markers and identified 13 QTLsassociated to the fiber quality in the F
2population derived
from the G hirsutum and G barbadense cross There arenumerous studies on using the RAPDs for QTL mappingalong with other molecular markers (Table 3) An extensiveSSR genotyping was conducted over F
2populations from 3
diverse upland cotton genotypes using 1378 markers and 39fiber related QTLs were identified [136] Recombinant inbredlines (RILs) are also important mapping populations andseveral QTLs related to plant architecture [137] yield [3] andfiber quality [19] have been identified in upland cotton usingRILs About 31QTLs linked to the yield and fiber quality traitsare detected bywide array of SSR and EST SSRmarkers (6123)in 4 way cross populations developed from the 4 inbred linesof G hirsutum [138] A genetic linkage map of the tetraploidcotton was developed using 1601 pairs of SSR and 247 SNPmarkers [139] The genetic map consisted of the 2072 locicovering 3380 cm of the cotton genome Two F
2populations
were generated by the crosses of upland cotton cultivars and4083 SSR markers were used for QTL analysis which detect54 QTLs linked to early maturity [140]
A total of 144 primer combinations of AFLPs and 150 ofSSRs were used to detect 28 QTLs related to the fiber traits[141] To know the significant threshold for the LR statisticspermutation tests were carried out afterwhich 7QTLs remainsignificant RIL lines developed from the intraspecific cross ofupland cotton are used to detect the 12 epistatic and 4 mainQTLs related to the plant architectural traits by 2130 SSR 2RAPD and 1 SRAP markers [137]
Conclusively huge arrays of QTLs have been identifiedusing multiple molecular marker technologies Descriptionof stable QTL from diverse generations common QTL fromvarious populations and homologous QTLs raises the infor-mation on the genetic base Information about distributionof important QTLs in the genome of cotton is very importantand promises the future strategy for marker assisted breed-ing Cotton Gen serves as an important database for suchinformation and currently this database has 988 QTLs for25 different traits (httpwwwcottongenorgdataqtl) whichcan be surveyed according to objectivity
33 Genome Wide Association Studies (GWAS) in CottonAssociation mapping also known as linkage disequilibrium(LD) mapping has appeared as a tool to determine thevariation in complex traits using historical and evolutionaryrecombination actions at the population level [142] In asso-ciation mapping nonstructured populations are phenotypedand genotyped to identify the trait associated with marker[143] This results into capture of wider recombination andhigher resolution mapping as compared to linkage mapping[144] The applications of association mapping for cottonassist extensive employment of natural genetic diversity con-served within the worldwide collections of cotton germplasm[145] as in other plant germplasm resources Turning theefforts of gene-tagging from biparental QTL mapping to LD-based association study promise the productive employment
of ex situ conserved genetic diversity of global germplasmresources of cotton [10] The cotton genome may need fewnumbers of markers for productive associating mappingof complex traits which is also reported for other crops[146] Regarding the tetraploid genome of cotton with atotal recombination length of about 5200 cm and an average400 kb per cm [22] the LD block sizes of sim5-6 cm distanceis sufficient to conduct an association mapping of differenttraits that would require a maximum of sim1000 polymorphicmarkers for successful and reliable associationmapping [147]Extent of genome-wide LD and association mapping offiber quality traits were reported using 95 SSR markers in285 exotic accessions of G hirsutum comprised of 208 lan-draces and 77 varieties [10] Similarly LD-based associationmapping was conducted for fiber quality traits in 335 Ghirsutum germplasm using 202 SSR markers [147] Progressin genome sequencing technology provides an opportunity toproduce large size genotypic data which supports associationmapping over QTL mapping and because of this associationmapping is becoming more common [148]
34 Marker Assisted Selection (MAS) in Cotton Markerassisted selection (MAS) is a procedure by which a phenotypeis selected on the basis of genotype of a marker [128]Selecting the plants in the segregating population that havethe suitable genes combinations is the important componentof plant breeding [149] Once the markers tightly linked tothe genes have been detected breeders may use particularDNA marker to identify the plants carry the genes [150]The effectiveness and cost of MAS are influenced by themarker technique therefore it must be selected carefully[151] During the past two decades RAPDs techniqueshave been used for MAS for getting the glanded plantsand glandless seeds in the interspecific population of Gsturtianum and other species [152] It was exposed that DNAmarkers connected to the major QTL (QTLFS1) for fiberstrength could be utilized inMAS to increase fiber strength ofcommercial varieties in segregating populations [153] SomeRAPD markers were developed into locus specific sequencecharacterized amplified region (SCAR) markers to screen theBC1F4upland cotton For example SCAR 1920marker for the
major fiber strength QTL was developed and has been usedfor selecting desirable genotypes [154] Screening of the SNPswhich aremapped on chromosome 10 recognized extra 3 SNPmarkers thatwere associatedwith blue disease resistance gene(Cbd) which were employed to efficiently characterize a traitallowing MAS for strong levels of blue disease resistance incotton breeding programs [155]
4 Cotton Draft Genome and Its Implication
The increasing information of DNA sequencing allows thediscovery of genes and molecular markers associated withdifferent traits opening new avenues for crop improvement[148] Sequencing of DNA promises to display the spectrumof diversity in the genus Gossypium The tetraploid cottonspecies (2119899 = 4119909 = 52) such as G hirsutum and G bar-
The Scientific World Journal 9
badense are thought to have developed by an allopoly-ploidization that happened nearly 1-2 million years ago inwhich a D-genome species is pollen parent and species of anA-genome is maternal parent [12 156] It is essential to havea basic awareness of the structure of the component genomesto understand the cultivated polyploid genomes their evo-lution and interaction between their subgenomes Towardthe long-term aim of characterizing the diversity amongcotton genomes the cotton geneticists have prioritized the Dgenome progenitor G raimondii for complete sequencing Graimondii has a sim880Mb genome [157] the smallest genomein the genus Gossypium at sim60 of the size of diploid A-genome and 40 of the tetraploids [158] A physical map ofG raimondii genome was assembled and several evidencesreferred that the G raimondii genome is composed of twodifferent qualitative components one that is gene-rich andanother that is repeat-rich [158] About 40976 protein codinggenes and 2355 syntenic blocks identified in the genome ofG raimondii [159] Similarly the sequencing and assemblingof G arboreum genome depicted that 685 of the genomeis covered by repetitive DNA sequences and about 41330protein-coding genes were predicted in the genome of Garboreum [160]
5 Future Prospects
Cotton is a major source of foreign exchange for manycountries around the globe therefore major focus remainsthe enhancement of yield and quality of fiber This challengecan be accomplished by introducing new alleles from wildspecies [161 162] and use of modern molecular technologieshelping in increasing genetic gain of economic traits In thisscenario it is believed that sequencing of the G raimondii[159] and G arboreum [160] draft genomes will facilitate thegene discovery of important traits These genome resourcescan also be used for discovery of high-throughput markerplatforms like Select SNP arrays These high-throughputDNAmarkers will be helpful in recognizing the cotton geno-types carrying desired characters and was successfully usednot only to study the genetic diversity but to develop linkagemaps and mapping agronomic traits [12 20] which arenecessary for acceleration of varietal development Althoughthe QTL mapping for the various traits that is fiber yieldand quality [131] drought tolerance [133] disease resistance[163 164] and pests resistance [165] have been accomplishedin cotton but these may not be helpful to clone causal genesdue to lower marker densities In general the choice of amolecular marker technique is based on reliability statisticalpower and level of polymorphisms Since their inventionthey are being continuously modified for improved utilityto solve many problems and to bring forth automationWhen these markers techniques reach a greater degree ofautomation then it will be suitable to use DNA markersdirecting to a new ldquoGreen Revolutionrdquo in the agriculturalworld
Presently the enormous development of more efficientDNAmarkers will go on in the future because they can serveas an important tool for the plant breeders and geneticists
to develop the cultivars of cotton that are demanded bythe society It has been proposed that SNPs marker willhave large influence on MAS and mapping studies in futuredue to high abundance and development of sophisticateddetection system [195] GBS will clearly become the markergenotyping platform in coming years So the development ofnovel markers such as GBS and SNPs and the accessibility ofmodern technologies such as DNA Chips and microarrayshasten genome mapping and subsequent gene discovery inthe cotton for efficient cotton varietal development
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgment
We are highly thankful to Dr Awais Rasheed (CIMMYTChina) for his valued inputs and comments
References
[1] USDA Cotton and Wool Year book Dataset 2011 httpusdamannlibcornelleduMannUsdaviewDocumentInfododocu-mentID=128
[2] K F Abdellatif Y A Khidr Y M Mansy M M Lawendey andY A Soliman ldquoMolecular diversity of Egyptian cotton (Gossyp-ium barbadense L) and its relation to varietal developmentrdquoJournal of Crop Science and Biotechnology vol 15 pp 93ndash992012
[3] T Zhang N Qian X Zhu et al ldquoVariations and transmissionof QTL alleles for yield and fiber qualities in upland cottoncultivars developed in Chinardquo PLoS ONE vol 8 no 2 ArticleID e57220 2013
[4] H J Kim and B A Triplett ldquoCotton fiber growth in plantaand in vitro Models for plant cell elongation and cell wallbiogenesisrdquo Plant Physiology vol 127 no 4 pp 1361ndash1366 2001
[5] Y-L Ruan D J Llewellyn and R T Furbank ldquoSuppressionof sucrose synthase gene expression represses cotton fiber cellinitiation elongation and seed developmentrdquo Plant Cell vol 15no 4 pp 952ndash964 2003
[6] Y-M Qin and Y-X Zhu ldquoHow cotton fibers elongate a tale oflinear cell-growth moderdquo Current Opinion in Plant Biology vol14 no 1 pp 106ndash111 2011
[7] P A Fryxell ldquoA revised taxonomic interpretation of GossypiumL (Malvaceae )rdquo Rheedea vol 2 pp 108ndash165 1992
[8] J O Beasley ldquoThe production of polyploids in gossypiumrdquoJournal of Heredity vol 31 no 1 pp 39ndash48 1940
[9] J E Endrizzi E L Turcotte and R J Kohel ldquoGenetics cytologyand evolution of Gossypiumrdquo Advances in Genetics vol 23 pp271ndash375 1985
[10] I Y Abdurakhmonov R J Kohel J Z Yu et al ldquoMoleculardiversity and associationmapping of fiber quality traits in exoticG hirsutum L germplasmrdquo Genomics vol 92 no 6 pp 478ndash487 2008
[11] J F Wendel and R C Cronn ldquoPolyploidy and the evolutionaryhistory of cottonrdquo Advances in Agronomy vol 78 pp 139ndash1862003
10 The Scientific World Journal
[12] Z J Chen B E Scheffler E Dennis et al ldquoToward sequencingcotton (Gossypium) genomesrdquo Plant Physiology vol 145 no 4pp 1303ndash1310 2007
[13] M J Iqbal O U K Reddy K M El-Zik and A E PepperldquoA genetic bottleneck in the lsquoevolution under domesticationrsquoof upland cotton Gossypium hirsutum L examined using DNAfingerprintingrdquoTheoretical and Applied Genetics vol 103 no 4pp 547ndash554 2001
[14] J O Beasley ldquoThe origin of American tetraploid GossypiumspeciesrdquoThe American Naturalist vol 74 pp 285ndash286 1940
[15] J O Beasley ldquoMeiotic chromosome behavior in species specieshybrids haploids and induced polyploids ofGossypiumrdquoGenet-ics vol 27 no 1 pp 25ndash54 1942
[16] J F Wendel C L Brubaker and A E Percival ldquoGeneticdiversity in Gossypium hirsutum and the origin of uplandcottonrdquoAmerican Journal of Botany vol 79 no 11 pp 1291ndash13101992
[17] A M Abdalla O U K Reddy K M El-Zik and A E PepperldquoGenetic diversity and relationships of diploid and tetraploidcottons revealed using AFLPrdquoTheoretical and Applied Geneticsvol 102 no 2-3 pp 222ndash229 2001
[18] X L Song X Z Sun T Z Zhang and H G Wang ldquoAdvanceson genetic diversity of cotton (Gossypium)rdquo Acta BotanicaBoreali-Occidentalia Sinica vol 24 pp 2393ndash2397 2004
[19] Z-S Zhang Y-H XiaoM Luo et al ldquoConstruction of a geneticlinkage map and QTL analysis of fiber-related traits in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 144 no 1-2 pp91ndash99 2005
[20] H-B Zhang Y Li BWang andPWChee ldquoRecent advances incotton genomicsrdquo International Journal of Plant Genomics vol2008 Article ID 742304 20 pages 2008
[21] K Arumuganathan and E D Earle ldquoNuclear DNA contentof some important plant speciesrdquo Plant Molecular BiologyReporter vol 9 no 3 pp 208ndash218 1991
[22] A H Paterson and R H Smith ldquoFuture horizons biotech-nology of cotton improvementrdquo in Cotton Origin HistoryTechnology and Production pp 415ndash432 John Wiley amp SonsNew York NY USA 1999
[23] V Tatineni R G Cantrell and D D Davis ldquoGenetic diversityin elite cotton germplasm determined by morphological char-acteristics and RAPDsrdquo Crop Science vol 36 no 1 pp 186ndash1921996
[24] C L Brubaker and J F Wendel ldquoRFLP diversity in cottonrdquo inGenetic Improvement of Cotton Emerging Technologies pp 81ndash101 Science Publishers Enfield NH USA 2001
[25] N D Young ldquoConstructing a plant genetic linkage map withDNA markersrdquo in DNA-Based Markers in Plants pp 39ndash57 Kluwer Academic Publishers Dordrecht The Netherlands1994
[26] M Agarwal N Shrivastava andH Padh ldquoAdvances inmolecu-lar marker techniques and their applications in plant sciencesrdquoPlant Cell Reports vol 27 no 4 pp 617ndash631 2008
[27] S Preetha and T S Raveendren ldquoMolecular marker technologyin cottonrdquo Biotechnology and Molecular Biology Reviews vol 3no 2 pp 32ndash45 2008
[28] J R Andersen and T Lubberstedt ldquoFunctional markers inplantsrdquo Trends in Plant Science vol 8 no 11 pp 554ndash560 2003
[29] R K Kalia M K Rai S Kalia R Singh and A K DhawanldquoMicrosatellite markers an overview of the recent progress inplantsrdquo Euphytica vol 177 no 3 pp 309ndash334 2011
[30] N Appleby D Edwards and J Batley ldquoNew technologiesfor ultra-high throughput genotyping in plantsrdquo Methods inMolecular Biology vol 513 pp 19ndash39 2009
[31] Q H Xu X L Zhang and Y C Nie ldquoGenetic diversityevaluation of cultivars (G hirsumtum L) from the Changjiangriver valley and Tellow river valley by RAPD markersrdquo ActaGenetica Sinica vol 28 no 7 pp 683ndash690 2001
[32] H J Lu and G O Myers ldquoGenetic relationships and discrim-ination of ten influential upland cotton varieties using RAPDmarkersrdquoTheoretical and Applied Genetics vol 105 no 2-3 pp325ndash331 2002
[33] I Alvarez and J F Wendel ldquoCryptic interspecific introgressionand genetic differentiation within Gossypium aridum (Mal-vaceae) and its relativesrdquo Evolution vol 60 no 3 pp 505ndash5172006
[34] S Liu RGCantrell J CMcCarty Jr and JM Stewart ldquoSimplesequence repeat-based assessment of genetic diversity in cottonrace stock accessionsrdquoCrop Science vol 40 no 5 pp 1459ndash14692000
[35] L F Zhu X L Zhang and Y C Nie ldquoAnalysis of geneticdiversity in upland cotton (Gossypium hirsutum L) cultivarsfrom China and foreign countries by RAPDs and SSRsrdquo Journalof Agricultural Biotechnology vol 11 pp 450ndash455 2003
[36] M P Reddy N Sarla and E A Siddiq ldquoInter simple sequencerepeat (ISSR) polymorphism and its application in plant breed-ingrdquo Euphytica vol 128 no 1 pp 9ndash17 2002
[37] C Schlotterer ldquoThe evolution of molecular markersmdashjust amatter of fashionrdquo Nature Reviews Genetics vol 5 no 1 pp63ndash69 2004
[38] C L Brubaker and J F Wendel ldquoReevaluating the origin ofdomesticated cotton (Gossypium hirsutum Malvaceae) usingnuclear restriction fragment length polymorphisms (RFLPs)rdquoAmerican Journal of Botany vol 81 no 10 pp 1309ndash1326 1994
[39] Z H Yu Y H Park G R Lazo and R J KohelMolecularMap-ping of the Cotton Genome Agron Abstracts ASA MadisonWis USA 1997
[40] C L Brubaker A H Paterson and J F Wendel ldquoComparativegenetic mapping of allotetraploid cotton and its diploid progen-itorsrdquo Genome vol 42 no 2 pp 184ndash203 1999
[41] M Ulloa and W R Meredith Jr ldquoGenetic linkage map andQTL analysis of agronomic and fiber traits in an intraspecificpopulationrdquo Journal of Cotton Science vol 4 no 3 pp 161ndash1702000
[42] M Ulloa W R Meredith Jr Z W Shappley and A L KahlerldquoRFLP genetic linkage maps from four F
23populations and
a joinmap of Gossypium hirsutum Lrdquo Theoretical and AppliedGenetics vol 104 no 2-3 pp 200ndash208 2002
[43] A J Reinisch J-M Dong C L Brubaker D M Stelly J FWendel and A H Paterson ldquoA detailed RFLP map of cottonGossypium hirsutum x Gossypium barbadense chromosomeorganization and evolution in a disomic polyploid genomerdquoGenetics vol 138 no 3 pp 829ndash847 1994
[44] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoD-subgenome bias of Xcm resistance genes in tetraploidGossypium (cotton) suggests that polyploid formation hascreated novel avenues for evolutionrdquo Genetics vol 149 no 4pp 1987ndash1996 1998
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are useful as geneticmarkersrdquoNucleic Acids Research vol 18 no22 pp 6531ndash6535 1990
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[48] K J Chalmers R Waugh J I Sprent A J Simons and WPowell ldquoDetection of genetic variation between and withinpopulations of Gliricidia sepium and G maculata using RAPDmarkersrdquo Heredity vol 69 pp 465ndash472 1992
[49] D S Multani and B R Lyon ldquoGenetic fingerprinting ofAustralian cotton cultivars with RAPD markersrdquo Genome vol38 no 5 pp 1005ndash1008 1995
[50] M KWajahatullah and J M Stewart ldquoGenomic affinity amongGossypium subgenus Sturtia species by RAPD analysisrdquo inProceeding of the Beltwide Cotton Conference National CottonCouncil p 452 Memphis Tenn USA 1997
[51] C D Geng Z Z Gong J Q Huang and Z C ZhangldquoIdentification of difference between cotton cultivars (G hirsu-tum) using the RAPD methodrdquo Jiangsu Journal of AgriculturalSciences vol 11 no 4 pp 21ndash24 1995
[52] T H Lan C G Cook and A H Paterson ldquoIdentification of aRAPDmarker linked tomale fertility restoration gene in cotton(Gossypium hirsutum L)rdquo Journal of Agricultural Genomics vol1 pp 1ndash5 1999
[53] B Shu K Fenling Z Y Yao Z G Mei Z Q Yuan and W XGang ldquoGenetic diversity analysis of representative elite cottonvarieties in three main cotton regions in China by RAPD andits relation with agronomic characteristicsrdquo Scientia AgriculturaSinica vol 34 pp 597ndash603 2001
[54] M Ulloa R G Cantrell R G Percy E Zeiger and Z Lu ldquoQTLanalysis of stomatal conductance and relationship to lint yieldin an interspecific cottonrdquo Journal of Cotton Science vol 4 no1 pp 10ndash18 2000
[55] B Bornet and M Branchard ldquoNonanchored inter simplesequence repeat (ISSR)markers reproducible and specific toolsfor genome fingerprintingrdquo Plant Molecular Biology Reportervol 19 no 3 pp 209ndash215 2001
[56] T M Culley and A D Wolfe ldquoPopulation genetic structureof the cleistogamous plant species Viola pubescens Aiton (Vio-laceae) as indicated by allozyme and ISSR molecular markersrdquoHeredity vol 86 no 5 pp 545ndash556 2000
[57] J B Wang ldquoISSR markers and their applications in plantgeneticsrdquo Yi Chuan vol 24 no 5 pp 613ndash616 2002
[58] T Nagaoka and Y Ogihara ldquoApplicability of inter-simplesequence repeat polymorphisms inwheat for use asDNAmark-ers in comparison to RFLP and RAPDmarkersrdquoTheoretical andApplied Genetics vol 94 no 5 pp 597ndash602 1997
[59] M Z Galvan B Bornet P A Balatti and M BranchardldquoInter simple sequence repeat (ISSR) markers as a tool for theassessment of both genetic diversity and gene pool origin incommon bean (Phaseolus vulgaris L)rdquo Euphytica vol 132 no3 pp 297ndash301 2003
[60] A Shi S Kantartzi M Mmbaga and P Chen ldquoDevelopmentof ISSR PCR markers for diversity study in dogwood (Cornusspp)rdquo Agriculture and Biology Journal of North America vol 1pp 189ndash194 2010
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[62] B Bornet C Muller F Paulus and M Branchard ldquoHighlyinformative nature of inter simple sequence repeat (ISSR)sequences amplified using tri- and tetra-nucleotide primersfrom DNA of cauliflower (Brassica oleracea var botrytis L)rdquoGenome vol 45 no 5 pp 890ndash896 2002
[63] M Sica G Gamba S Montieri L Gaudio and S AcetoldquoISSR markers show differentiation among Italian populationsofAsparagus acutifolius Lrdquo BMCGenetics vol 6 article 17 2005
[64] P Vos R Hogers M Bleeker et al ldquoAFLP a new technique forDNA fingerprintingrdquo Nucleic Acids Research vol 23 no 21 pp4407ndash4414 1995
[65] G O Myers B Jiang M W Akash A Badigannavar and SSaha ldquoChromosomal assignment of AFLP markers in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 165 no 2 pp391ndash399 2009
[66] K Lukonge L Hersalman and M T Labuschagne ldquoGeneticdiversity of tanzanian cotton revealed by AFLP analysisrdquo inProceedings of the African Crop Science Conference vol 8 pp773ndash776 2007
[67] N Murtaza ldquoCotton genetic diversity study by AFLP markersrdquoElectronic Journal of Biotechnology vol 9 no 4 pp 456ndash4602006
[68] M Zhong J CMcCarty J N Jenkins and S Saha ldquoAssessmentof day-neutral backcross populations of cotton using AFLPmarkersrdquo Journal of Cotton Science vol 6 no 2 pp 97ndash1032002
[69] A Rakshit S Rakshit J Singh et al ldquoAssociation of AFLPand SSR markers with agronomic and fibre quality traits inGossypium hirsutum Lrdquo Journal of Genetics vol 89 no 2 pp155ndash162 2010
[70] A Badigannavar and G Myers ldquoGenetic analysis of AFLPmarkers associated with seed quality traits in upland cotton(Gossypium hirsutum)rdquo in Beltwide Cotton Conferences NewOrleans La USA 2010
[71] M K Altaf J M C D Stewart M K Wajahatullah J Zhangand R G Cantrell ldquoMolecular and morphological geneticsof a trispecies F2 population of cottonrdquo in Proceedings of theBeltwide Cotton Conferences vol 1 pp 448ndash452 New OrleansLa USA January 1997
[72] M K Rana and K V Bhat ldquoA comparison of AFLP andRAPD markers for genetic diversity and cultivar identificationin cottonrdquo Journal of Plant Biochemistry and Biotechnology vol13 no 1 pp 19ndash24 2004
[73] J-M Lacape T-B Nguyen S Thibivilliers et al ldquoA combinedRFLP-SSR-AFLP map of tetraploid cotton based on a Gossyp-ium hirsutum times Gossypium barbadense backcross populationrdquoGenome vol 46 no 4 pp 612ndash626 2003
[74] D TautzM Trick andG A Dover ldquoCryptic simplicity in DNAis amajor source of genetic variationrdquoNature vol 322 no 6080pp 652ndash656 1986
[75] S Saha J Wu J N Jenkins et al ldquoBreeding and genetics effectof chromosome substitutions from Gossypium barbadense L 3-79 into G hirsutum L TM-1 on agronomic and fiber traitsrdquoJournal of Cotton Science vol 8 no 3 pp 162ndash169 2004
[76] O U K Reddy A E Pepper I Abdurakhmonov et al ldquoNewdinucleotide and trinucleotide microsatellite marker resourcesfor cotton genome researchrdquo Journal of Cotton Science vol 5no 2 pp 103ndash113 2001
[77] T B Nguyen M Giband P Brottier A M Risterucci and JM Lascape ldquoWide coverage of the tetraploid cotton genomeusing newly developed microsatellite markersrdquoTheoretical andApplied Genetics vol 109 no 1 pp 167ndash175 2004
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[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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PeptidesInternational Journal of
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International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
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BioinformaticsAdvances in
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Signal TransductionJournal of
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Evolutionary BiologyInternational Journal of
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ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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The Scientific World Journal 3
can not only amplify small quantity of DNA but degradedsources of DNA can also be amplified [45] The reactionof PCR consists of many cycles of denaturation annealingand extension Then the PCR product can be visualizedon agarose or polyacrylamide gels PCR-based technologyhas been utilized widely in analysis of genetic diversity andrecognition of DNA markers Due to the simplicity and highchances of success in PCR many approaches for productionof PCR based molecular markers were described
221 Random Amplified Polymorphic DNA RAPD RAPD isan old PCR based technique that infers DNA polymorphismsdue to deletions or reorganization between the obligatingsites of oligonucleotide primer in the genome [46] InRAPDsDNA fragments are amplified by the PCR reaction usingrandom primers (usually of 10 bp) [47] The sequence ofthe RAPD primers must fulfill the following criteria (i)minimum 40 GC contents and (ii) absence of palindromicsequence [46] A discrete DNA product is produced if thesepriming sites are within an amplifiable range of each other
RAPD techniques have been used for many purposesincluding assessment of genetic variations in population[23 48] DNA fingerprinting [49] and determining therelationship between the genotypes of different and samespecies [50] In cotton RAPDs were used to distinguish thecotton varieties resistant to jassids aphids and mites [51]RAPD marker (R-6592) for the male sterility gene has beenidentified in cotton [52] RAPD techniques are also usedto evaluate the genetic relationship among cotton genotypes[53] to identify the QTLs for stomatal conductance [54] andto construct linkage mapping in cotton
222 Inter Simple Sequence Repeats ISSR In ISSRs DNAfragments are amplified which present between two identicalSSRs directed in contrary directions [47] It allows thedetection of polymorphism in inter SSR loci using primer(16ndash25 bp long) complimentary to a single SSR and annealat either the 31015840 or 51015840 end [47] that can be di tri tetraor pentanucleotide [36] The ISSR primers are commonlyanchored at 31015840 or 51015840 end with 1 to 4 bases stretched into theflanking regions The primers anchored at 31015840 end producemore obvious bands as compared to anchored at 51015840 end [36]The technique of ISSR markers combines many benefits ofAFLPs and SSRs with universality of RAPDs [55] Generallythe sequence of ISSR primers is larger as compare to RAPDprimers allowing higher annealing temperature which out-comes greater reproducibility of bands than RAPDs [36 56]Amplification of ISSRs also revealed larger fragments numberper primer than RAPDs [57] Many earlier studies reportedthat ISSR markers were more informative than RAPDs forgenetic diversity evaluation in different crop species [58 59]
The applications of ISSRs for different purposes dependon the diversity and frequencies of SSR within the particulargenomes [60] It is quickly being utilized by the researchcommunity in different areas of plant improvement that isin gene tagging analysis of genetic diversity and estimationof SSR motif [61ndash63]
223 Amplified Fragment Length Polymorphism AFLPAFLP markers were developed to overcome the problem ofreproducibility connected to RAPDs [64] This techniquedetects large number of loci in a single reaction of PCR [6465] and discovers large number of polymorphism dispersedacross the genome [66] In AFLP assays amplicon numbersare depend on (i) number of selective nucleotides in theprimer (ii) selective nucleotide motif (iii) GC content and(iv) physical genome size [26] AFLP is an effective toolfor the observation of genetic diversity [67] fingerprintingstudies and tagging of agronomic seed and fiber qualitytraits [68ndash70] AFLP is a great valued technique for genemapping studies due to their high abundance and randomdistribution throughout the genome [64] A linkage map ofcotton was developed using the AFLP and RAPD markers[71] AFLP markers have also been used for analyzing thegenetic diversity [17 72] andmap saturation in cotton [19 73]
224 Microsatellites or Simple Sequence Repeats SSR Theseare di- tri- tetra- or pentatandom repeats of nucleotidescattered abundantly in both noncoding and coding regionsof a genome [29 47] Microsatellites are created from spherewhere variants of repetitive DNA sequence are previouslyoverrepresented [74] The loci of these markers are highlytransferable about 50 across species [75] For SSRs analysisforward and reverse primers are employed in PCR reactionthat anneal to the template DNA at the 51015840 and 31015840 ends Shortrepetitive DNA sequences furnish the basis for multi alleliccodominant PCR based molecular marker and found morepolymorphic as compare to other DNA markers [27 47]
Due to their greater polymorphism SSRs are consideredas an important marker system in fingerprinting analysisof genetic diversity molecular mapping and marker assistedselection [76] The availability of SSR markers in the cottongenome make them useful in study of genetic diversity [20]Furthermore over 1000 SSR primers have been designedfrom available cotton DNA sequences in genomic libraries[77] Cotton Gen database is the largest repository for theSSR markers and their mapping information (httpwwwcottongenorgfindmapped markers)
(1) EST-SSRs SSR markers obtained from ESTs (expressedsequence tags) are present in sequences of functional geneand directly associated with transcribed parts of DNA [78]About 1ndash5 of the ESTs in different species of plants haveSSRs of suitable length for development of markers [79] Ascompare to genomic SSRs EST-SSR markers have greaterpotential for transferability between the species [80] EST-SSRs also have a greater possibility of being functionallylinked with variations in gene expression than genomicSSRs [81] Rising number of ESTs for cotton helped in therecognition of SSRs domains from the ESTs by data miningmethods Recently several EST-SSRs have been mappedin cotton [82ndash85] However EST-SSRs exhibit low level ofpolymorphism than conventional SSRs [86]
(2) CAPS Microsatellites Cleaved amplified polymorphicsequence (CAPS) technique is actually the combination of
4 The Scientific World Journal
RFLP and PCR [87] in which DNA fragments are ampli-fied through PCR followed by digestion with a restrictionenzyme [88] Subsequently polymorphisms arise from thevariation in the incidence of restriction sites of identi-fied alleles are detected by gel electrophoresis [88] CAPSmicrosatellite and CAPS are technically alike and use ofmicrosatellite spheres and flanking regions as a templatemay have a decisive improvement over the well-known DNAmarkers in crop species CAPS microsatellites change themonomorphic markers into polymorphic markers whichmostly inherited in codominant way [89] and exhibit highpolymorphism between strongly related genotypes Any basesubstitutions can be identified by CAPS microsatellites as thepolymorphism exhibited by this technique is based on thesequence dissimilarities in the flanking regions aside fromthe microsatellite spheres These markers also assist in theanalysis of composite traits by genemapping and propose theopportunity of identifying markers by physiological and bio-chemical characteristics of their gene products [86]Howeverthe CAPSmarkers are only developedwheremutations createa recognition site for restriction enzyme [87]
23 Sequence Based DNAMarkers
231 Single Nucleotide Polymorphism Variations of singlenucleotide (A T C G) in sequence of individual genomeare known as single nucleotide polymorphism or SNPs [26]These may occur in the noncoding coding and intergenicregions of the genome so allowing the detection of the genesdue to the variations in the sequences of nucleotides [26 90]and these are either nonsynonymous or synonymous withinthe coding regions of the genome Synonymous changes canalter mRNA splicing that result the changes in the phenotypeof an individual [91]
SNP markers are important tool for linkage mappingmap based cloning and marker assisted selection due to thehigh level of polymorphismThe codominant nature of SNPsmakes thesemarkers able to distinguish the heterozygous andhomozygous alleles [92] Narrow genetic base and allotetrap-loid genome has made the discovery of SNPs difficult incotton [93] Recently use of high throughput sequencingtechniques have made it possible to detect great numbersof SNP markers [94 95] including organisms with limitedmolecular studies [96 97] and organisms with slight geneticvariation such as cotton [85] In cotton many researcheshave been conducted to observe diversity characteriza-tion and mapping of SNPs in the nucleotide sequenceof Gossypium genome [98 99] Recently an internationalcollaborative effort has developed 70K SNP chip basedon Illumina Infinium genotyping assay (Unpublished datahttpwwwcottongenorgnode1287616)This high-through-put genotyping assay will be a resource that will be usedglobally by public and private breeders geneticists and otherresearchers to enhance cotton genetic analysis breedinggenome sequence assembly and many other uses SimilarlyGene Chip cotton genome array comprising of 239777 probesets representing 21485 cotton transcripts has been developedand under validation step before commercially available by
Affymetrix (httpwwwaffymetrixcomproducts servicesarraysspecificcottonaffx)The sequences used for SNP chipdevelopment were selected from GenBank dbEST and Ref-Seq contributed by the collaborators globally These high-throughput technologies will be helpful for fine mapping andsubsequent gene discovery for important economic traits incotton Additionally these resources will provide foundationsto initiate genomic selection studies in cotton ultimatelyenhancing genetic gain from breeding
232 Genotyping by Sequencing GBS Genotyping-by-se-quencing (GBS) is a technique that simultaneously detectsand genotypes the SNPs in a genome [100] GBS was devel-oped as a simple but strong access for reducing complexityin complex genomes [101] The development of the GBSlibrary is very simpleThe original GBS method used a singlerestriction enzyme to capture the genomic sequence betweenrestriction sites [101]
The choice of restriction enzyme is a crucial factor inGBS for covering the repetitive regions in the genomesIn the original GBS approach used in maize and barleyone restriction enzyme (RE) ldquoApeKIrdquo was used which ismethylation-sensitive to reduce the complexity of the genomeand to choose hypomethylated sphere of the genome forsequencing [101] A modified GBS approach was also devel-oped in which two enzymes and a Y-adapter were usedto generate ldquouniformrdquo GBS libraries where Adapter 1 andAdapter 2were on opposite ends of every fragment [102] GBSis a multiple approach that can discover thousands of SNPs inan experiment and suitable for population studies genomicselection genetic mapping germplasm characterization andother breeding applications in different organisms [101ndash103]GBS technique can also be employed in species of plants thatdo not have available reference genome In these cases thesequence tags can be deal as dominant markers for analysis[100]
3 Overview of Marker Based CropImprovement Efforts
31 Genetic Diversity in Cotton The success of any breedingprogram mainly depends on the availability of the geneticdiversity in the germplasm resources Understanding of thegenetic relationships among plant genotypes is significantto know the complexity of available germplasm to discoverthe differences in available genotypes and to build up usefulconservation plans [104] Thus evaluation based on themolecular markers can give valuable insight into the geneticstructure of a plant population which helps in the devel-opment of new varieties [105] The genetic diversity studiesin cotton germplasm using different marker technologies aresummarized in Table 2 A narrow genetic base is reported incotton by several workers using different molecular markers[23 38 49 106 107]
RAPD and ISSR techniques have been utilized to analyzegenetic diversity and hybridization and for the incident ofsomaclonal variations in various crops involving cotton [108ndash112] Five prominent studies were conducted to evaluate
The Scientific World Journal 5
Table2Anoverview
ofgenetic
diversity
studies
incotto
nusingmolecular
markers
Marker
Cou
ntry
Popu
latio
ntype
Size
References
RAPD
s
USA
16near-hom
ozygou
selitec
ottongeno
types
80RA
PDprim
ers
[23]
Pakista
n31
Gossypium
species3subspecies
and1interspecifich
ybrid
45RA
PDprim
ers
[115]
USA
10varie
tieso
fUplandcotto
n86
RAPD
prim
ers
[32]
Pakista
n30
cultivarsof
Garboretum
50RA
PDprim
ers
[169]
Iran
13F 1
andF 2
cotto
ngeno
types(Gossypium
hirsutum
)obtainedby
crossin
g30
RAPD
prim
ers
[170]
India
Intraspecific
cotto
nF 1
hybrid
andits
parents
20RA
PDprim
ers
[171]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
40RA
PDprim
ers
[172]
SSRs
USA
24cultivarsof
Ghirsutum
88SSRprim
ers
[173]
China
39accessions
ofG
arboreum
358SSRprim
ers
[174]
China
108accessions
ofAs
iatic
cotto
nand1G
herbaceum
60SSRprim
ers
[175]
China
43sourceso
fUplandcotto
ngerm
plasm
36SSRprim
ers
[124]
France
47geno
typeso
ftetraploidcotto
n320SSRprim
ers
[176]
USA
96accessions
ofG
arboreum
115Genom
icandES
T-SSRs
[177]
Pakistan
8accessions
ofG
hirsutum
32SSRprim
ers
[178]
China
59geno
typeso
fGhirsutum
40ES
T-SSRprim
ers
[179]
Greece
29geno
typeso
fGhirsutum
andan
interspecific
hybrid
12SSRprim
erpairs
[180]
China
56accessions
ofSeaisla
ndcotto
n237SSRprim
ers
[125]
Egypt
28geno
typeso
fEgyptiancotto
n6SSRand5ES
T-SSRprim
er[2]
Pakista
n19
geno
typeso
fBtcotton
104SSRprim
ers
[107]
USA
193cultivarsof
Uplandcotto
n44
8SSRprim
ers
[126]
USA
378accessions
ofG
hirsutum
and3of
Gbarbadense
120SSRprim
ers
[181]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
4SSRprim
ers
[172]
AFL
Ps
USA
11accessions
ofG
hirsutum
and2fro
meach
ofG
arboreum
Gherbaceum
andG
barbadense
4EcoR
I-MseIp
rimersfor
AFL
P[106]
Belgium
Uplandcotto
nwild
species(G
raim
ondiiand
Gthurbrii)
andtheirB
C 3progenies
5AFL
Pprim
ers
[117]
USA
3diploidspecieso
fGossypium
3G
barbadensecultivarsand43
Ghirsutum
accessions
20AFL
Pprim
ers
[13]
USA
29accessions
from
fives
pecies
oftheg
enus
Gossypium
16AFL
Pprim
ers
[17]
India
24lin
esof
Ghirsutum
L6AFL
Pprim
ers
[182]
Norway
131a
ccessio
nsof
Gbarbadan
se8AFL
Pprim
ers
[183]
ISSR
s
Iran
13F 1
andF 2
cotto
ngeno
types(Gossypium
hirsutum
)8ISSR
prim
ers
[170]
Egypt
28Eg
yptia
ncotto
ngeno
types
5ISSR
prim
ers
[2]
India
Intraspecific
cotto
nF 1
hybrid
andits
parents
19ISSR
prim
ers
[171]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
20ISSR
prim
ers
[172]
SNPs
Pakista
n2cultivarsof
tetraploid
cotto
nPrim
ersc
orrespon
dto
FIF1
gene
[184]
USA
24lin
esof
cotto
n270SN
Plociand92
Indel
[99]
6 The Scientific World Journal
genetic diversity using RAPD markers during 90s Geneticdiversity of 16 elite homozygous genotypes obtained fromthe inter-specific hybridization was studied using 80 RAPDmarkers [23] RAPD markers were used to differentiate theG hirsutum lines from the G arboretum [113] Similarly25 short duration genotypes of cotton were analyzed usingarbitrary primers [114] Later [115] studied genetic diversityof 31 Gossypium species 3 subspecies and 1 interspecifichybrid using 45 RAPD primers and the results showed thatgenetic relationship of many species is related to the centerof origin Recently genetic diversity in 18 cotton genotypes ofPakistan studied by 5 RAPD primers showed that two diversegenotypes of cotton (CIM-240 and CIM-443) have resistanceagainst cotton leaf curl virus [116]
AFLP technique was also used to distinguish the dif-ferences among diploid and tetraploid species of cotton byutilizing the variations in ribosomal RNA genes [106] Thegenetic diversity between the upland cotton wild species (Graimondii G thurberii and G sturtianum) and their BC
3
progenies was evaluated usingAFLPmarkers [117] Intra- andinterspecific relatedness of theG barbadense G arboreumGraimondii and G hirsutum are determined by AFLPs whichdemonstrated its usefulness for genetic relatedness acrosswide range of species [17] The relationship between the par-ents and four day neutral backcross generations of cotton wasdetermined using 43 AFLP markers [68] Comparative studywas conducted to evaluate AFLP and RAPD techniques using16 diploid cotton genotypes and it was concluded that AFLPmarkers are more efficient for polymorphism detection andfor analyzing of genetic diversity as compared to RAPDs [72]Similarly genetic diversity of 26 Tanzanian cotton genotypes(Gossypiumhirsutum L) was studied using theAFLPmarkers[66] The results of this study indicated the high values ofgenetic similarity which show the lower genetic diversityamong Tanzanian cotton cultivars Reference [65] mapped98 AFLP markers and assigned 22 distinctive chromoso-mal positions using cytogenetic deletion stocks Mappinginformation enhanced the utilization of AFLPs and can beused to saturate the existing marker frequency over differentchromosomes
In cotton SSRs are considered as a new class of DNAmarkers which hastened cotton genetic diversity and map-ping studies [27] and are important source to observe thetranscribed genes [118] There are multiple reports aboutusing the SSR markers for genetic diversity Reference [119]identified 71 SSR loci with 65 primer pairs and placed themondistinctive chromosomes of cotton Genetic diversity amongUS and Australian cultivars and day neutral lines of Ghirsutum was also analyzed by SSR markers [120]
Further saturation of SSR markers was extended by addi-tion of 204 markers which exhibited 261 segregating bandsgiving rise to 233 mapped loci in cotton [77] Interspecificpolymorphism between G barbadense and G hirsutum wasalso studied using SSR markers and results showed thatpolymorphism between species was high but it was lowwithin species [121] Reference [122] developed new SSRmarkers analyzed the status of 23 chromosomes and foundthat the inter loci distance was 49 cM Diversity among52 different G hirsutum cultivars was studied by 31 SSR
primer pairs and successfully discriminated the 52 cultivarsthrough broader allelic coverage [123] Similarly geneticdiversity of 43 upland cotton varieties [124] 56 sea-islandcotton accessions [125] 19 Bt cotton genotypes [107] 50representative Pakistani genotypes [104] and 193 uplandcotton cultivars [126] were evaluated using 36 237 104 70and 448 SSR markers respectively SSRs have also been usedto assess the genetic purity of the cotton hybrids [127] anddemonstrated as an effective tool for hybrid identification
Recent developments in next generation sequencing(NGS) and RNA-seq technology have generated high-throughput sequence data which facilitated the identificationof SNPs as effective and highly saturated markers for geneticstudies in cotton Genetic variations within and betweenthe different species of cotton have been characterized by1000 SNPs and 279 In-Dels from the 270 and 92 locisegregating in G barbadense and G hirsutum to providemapped molecular markers for crosses within species andintrogression of foreign germplasm in cotton [99] A genomereduction experiment based on the restriction site conserva-tion (GR-RSC) and previously generated assembly of expresssequence tags (ESTs) were used to discover the SNPs in 4accessions of G hirsutum and G barbadense A total 11834and 1679 non-genic and 4327 genic SNPs were identified inthe GR-RSC and EST assemblies using highly conservationparameters The KASPer assays were used to target the 1052(704 nongenic and 348 genic) genome specific SNPs betweenthe G hirsutum accessions [93] The assay then tested forthe Mendelian segregation ratio in the F
2population derived
from a cross of upland cotton (G hirsutum) cultivars
32 QTLs Mapping for Important Economic Traits in Cot-ton The regions in genomes to have genes linked with aquantitative trait are known as quantitative trait loci QTLs[128] and the process of developing linkage maps andperforming QTL analysis is referred to as QTLmapping [129130] QTL analysis stands on the principal of identifying aconnection among phenotype and genotype ofmarkers [128]The QTLs identified in cotton germplasm using differentmarker technologies are summarized in Table 3
RFLPs have been widely used to map genes of economicinterest in cotton Previously RFLP map of G hirsutum andG barbadensewas used tomap 14QTLs for fiber related traits[131] Similarly genes influencing density of stem and leaftrichomes [132] high gossypol plant and low seed gossypolcontents [117] were confined by RFLP markers Reference[131] developed an RFLP map of 261 markers distributedamong 26 linkage groups using F
2plants from an interspecific
cross Another genetic linkage map was developed usingRFLP markers and 26 QTLs were recognized for agronomicand fiber quality traits [41] Later on RFLP based QTLmapping was extended to leaf chlorophyll contents [133]Backcross population of G hirsutum and G barbadense wasused to map 28 9 and 8 QTLs for fiber length lengthuniformity and short fiber contents respectively using the262 RFLP markers [134]
RAPDs have also been widely used for QTL mappingin cotton however lack of reproducibility and unknown
The Scientific World Journal 7
Table3Anoverview
ofQTL
studies
incotto
n
Traits
Descriptor
Popu
latio
nSize
Marker(nu
mbera
ndtype)
QTL
snum
ber
Reference
Fiberq
uality
FSFLandFF
F 2171
RFLP
sand
85RA
PDs
13[135]
FSF 2
186
217SSRs800
RAPD
sUBC
and1040
OPE
RON
2[153]
LYLPSW
NSUQSFFL
FE
FTFFandIF
F 2120
144AFL
PsR
FLPs
and150SSRs
28[14
1]FS
FE
FLFU
LPandFF
F 2117
290SSRs
and9AFL
Ps16
[19]
FFBC
3F2
3662
262RF
LPs
41[185]
FLFLU
andSFC
BC3F
23662
262RF
LPs
45[134]
FSFE
FUFLandFF
RILrsquos
270
7508
SSRs384
SRAPs
and740IT-ISJs
13[186]
FLFSFF
andFE
F 2mdash
1378
SSRs
39[136]
FSFLFFFMTFE
andSFI
RILrsquos
180
4106
SSRsA
FLPsR
APD
sand
SRAPs
48[187]
FEFLFS
FFandFU
CP172
16052SSRs
63[188]
Fibera
ndagrono
mical
SCYLYLPBW
SIFM
TPE
RWFWTFFFLFE
andFS
RILrsquos
188
141S
SRs
56[189]
Yield
andfib
er
FSFLFFFE
LPSINB
SCYandLY
RILrsquos
258
2131
SSRs
53[19
0]
NB
BWSILPLISC
YLYFLFS
FFFE
andFU
4WCandinbred
lines
280
6123
SSRs
andES
T-SSRs
31[138]
SCYLYN
BBW
LPSILIand
FBN
RILrsquos
andIF2
180
2675
EST-SSRs
111
[191]
PHFBN
BWLPLISILYFLFS
FE
FFandFU
Ghirsutum
accessions
81121S
SRs
180
[3]
LISILYSCY
NSB
andFS
F 269
834SSRs437
SRAPs107
RAPD
sand
16RE
MAPs
52[192]
Morph
ological
LBNOSL1L1W1L2
W2L3
andW3
F 2180
261R
FLPs
62[19
3]EM
F 2andF 3
mdash40
83SSRs
54[14
0]NFB
F 2251
1165SSRs
5[19
4]Plant
architectural
PHFBL
FBN
FBA
FBL
PHandNMUB
RILrsquos
180
2130
SSRs2
RAPD
sand
1SRA
P16
[137]
NB
numbero
fbollsperp
lantB
Wb
ollw
eightSIseedindexLP
lintp
ercentL
Ilin
tind
exSIseed
indexSC
Yseed
cotto
nyieldperp
lantLY
linty
ield
perp
lantF
Lfib
erleng
thF
Sfib
erstr
ength
FEfi
ber
elong
ation
FUfiberu
niform
ityratio
FY
fiber
yello
wnessFFfib
erfin
enessFM
Tfib
ermaturityP
Hplant
heightFBL
fruitbranch
leng
thFBN
fruitbranch
numberFB
Afruitbranch
angleFL
Ufiberlength
unifo
rmitySFC
sho
rtfib
ercontentFR
fiberreflectanceSW
seedweightNSnu
mbero
fseeds
perp
lantU
Qupp
erqu
artilelengthSFsho
rtfib
ercontentFT
fibertenacityIFim
maturefi
bercon
tentSFIsho
rtfib
erindexNSB
num
bero
fseeds
perb
ollEM
earlymaturityN
MUB
lowerm
iddleandup
sideb
olln
umberNFB
nod
etofirstfruitin
gbranchLBN
Olob
enum
bersSL1sub
lobe
numbero
nthem
ainlobeL1
main-lobe
leng
thW
1main-lobe
widthL2second
-lobe
leng
thW
2second
-lobe
widthL3third
-lobe
leng
thW
3third
-lobe
leng
thPER
perim
eterW
Fweightfi
tnessWT
wallthicknessFBL
PHratioof
fruit
branch
leng
thto
planth
eightRILrsquosrecom
binant
inbred
linesIF2immortalized
F2s4W
Cfour
way
crossCP
com
positec
rossand
BC3F
2=backcrossfam
ilies
8 The Scientific World Journal
chromosomal positions remained main disadvantages whichrestricted the use of RAPDs in advanced studies Refer-ence [135] used 85 RAPD markers and identified 13 QTLsassociated to the fiber quality in the F
2population derived
from the G hirsutum and G barbadense cross There arenumerous studies on using the RAPDs for QTL mappingalong with other molecular markers (Table 3) An extensiveSSR genotyping was conducted over F
2populations from 3
diverse upland cotton genotypes using 1378 markers and 39fiber related QTLs were identified [136] Recombinant inbredlines (RILs) are also important mapping populations andseveral QTLs related to plant architecture [137] yield [3] andfiber quality [19] have been identified in upland cotton usingRILs About 31QTLs linked to the yield and fiber quality traitsare detected bywide array of SSR and EST SSRmarkers (6123)in 4 way cross populations developed from the 4 inbred linesof G hirsutum [138] A genetic linkage map of the tetraploidcotton was developed using 1601 pairs of SSR and 247 SNPmarkers [139] The genetic map consisted of the 2072 locicovering 3380 cm of the cotton genome Two F
2populations
were generated by the crosses of upland cotton cultivars and4083 SSR markers were used for QTL analysis which detect54 QTLs linked to early maturity [140]
A total of 144 primer combinations of AFLPs and 150 ofSSRs were used to detect 28 QTLs related to the fiber traits[141] To know the significant threshold for the LR statisticspermutation tests were carried out afterwhich 7QTLs remainsignificant RIL lines developed from the intraspecific cross ofupland cotton are used to detect the 12 epistatic and 4 mainQTLs related to the plant architectural traits by 2130 SSR 2RAPD and 1 SRAP markers [137]
Conclusively huge arrays of QTLs have been identifiedusing multiple molecular marker technologies Descriptionof stable QTL from diverse generations common QTL fromvarious populations and homologous QTLs raises the infor-mation on the genetic base Information about distributionof important QTLs in the genome of cotton is very importantand promises the future strategy for marker assisted breed-ing Cotton Gen serves as an important database for suchinformation and currently this database has 988 QTLs for25 different traits (httpwwwcottongenorgdataqtl) whichcan be surveyed according to objectivity
33 Genome Wide Association Studies (GWAS) in CottonAssociation mapping also known as linkage disequilibrium(LD) mapping has appeared as a tool to determine thevariation in complex traits using historical and evolutionaryrecombination actions at the population level [142] In asso-ciation mapping nonstructured populations are phenotypedand genotyped to identify the trait associated with marker[143] This results into capture of wider recombination andhigher resolution mapping as compared to linkage mapping[144] The applications of association mapping for cottonassist extensive employment of natural genetic diversity con-served within the worldwide collections of cotton germplasm[145] as in other plant germplasm resources Turning theefforts of gene-tagging from biparental QTL mapping to LD-based association study promise the productive employment
of ex situ conserved genetic diversity of global germplasmresources of cotton [10] The cotton genome may need fewnumbers of markers for productive associating mappingof complex traits which is also reported for other crops[146] Regarding the tetraploid genome of cotton with atotal recombination length of about 5200 cm and an average400 kb per cm [22] the LD block sizes of sim5-6 cm distanceis sufficient to conduct an association mapping of differenttraits that would require a maximum of sim1000 polymorphicmarkers for successful and reliable associationmapping [147]Extent of genome-wide LD and association mapping offiber quality traits were reported using 95 SSR markers in285 exotic accessions of G hirsutum comprised of 208 lan-draces and 77 varieties [10] Similarly LD-based associationmapping was conducted for fiber quality traits in 335 Ghirsutum germplasm using 202 SSR markers [147] Progressin genome sequencing technology provides an opportunity toproduce large size genotypic data which supports associationmapping over QTL mapping and because of this associationmapping is becoming more common [148]
34 Marker Assisted Selection (MAS) in Cotton Markerassisted selection (MAS) is a procedure by which a phenotypeis selected on the basis of genotype of a marker [128]Selecting the plants in the segregating population that havethe suitable genes combinations is the important componentof plant breeding [149] Once the markers tightly linked tothe genes have been detected breeders may use particularDNA marker to identify the plants carry the genes [150]The effectiveness and cost of MAS are influenced by themarker technique therefore it must be selected carefully[151] During the past two decades RAPDs techniqueshave been used for MAS for getting the glanded plantsand glandless seeds in the interspecific population of Gsturtianum and other species [152] It was exposed that DNAmarkers connected to the major QTL (QTLFS1) for fiberstrength could be utilized inMAS to increase fiber strength ofcommercial varieties in segregating populations [153] SomeRAPD markers were developed into locus specific sequencecharacterized amplified region (SCAR) markers to screen theBC1F4upland cotton For example SCAR 1920marker for the
major fiber strength QTL was developed and has been usedfor selecting desirable genotypes [154] Screening of the SNPswhich aremapped on chromosome 10 recognized extra 3 SNPmarkers thatwere associatedwith blue disease resistance gene(Cbd) which were employed to efficiently characterize a traitallowing MAS for strong levels of blue disease resistance incotton breeding programs [155]
4 Cotton Draft Genome and Its Implication
The increasing information of DNA sequencing allows thediscovery of genes and molecular markers associated withdifferent traits opening new avenues for crop improvement[148] Sequencing of DNA promises to display the spectrumof diversity in the genus Gossypium The tetraploid cottonspecies (2119899 = 4119909 = 52) such as G hirsutum and G bar-
The Scientific World Journal 9
badense are thought to have developed by an allopoly-ploidization that happened nearly 1-2 million years ago inwhich a D-genome species is pollen parent and species of anA-genome is maternal parent [12 156] It is essential to havea basic awareness of the structure of the component genomesto understand the cultivated polyploid genomes their evo-lution and interaction between their subgenomes Towardthe long-term aim of characterizing the diversity amongcotton genomes the cotton geneticists have prioritized the Dgenome progenitor G raimondii for complete sequencing Graimondii has a sim880Mb genome [157] the smallest genomein the genus Gossypium at sim60 of the size of diploid A-genome and 40 of the tetraploids [158] A physical map ofG raimondii genome was assembled and several evidencesreferred that the G raimondii genome is composed of twodifferent qualitative components one that is gene-rich andanother that is repeat-rich [158] About 40976 protein codinggenes and 2355 syntenic blocks identified in the genome ofG raimondii [159] Similarly the sequencing and assemblingof G arboreum genome depicted that 685 of the genomeis covered by repetitive DNA sequences and about 41330protein-coding genes were predicted in the genome of Garboreum [160]
5 Future Prospects
Cotton is a major source of foreign exchange for manycountries around the globe therefore major focus remainsthe enhancement of yield and quality of fiber This challengecan be accomplished by introducing new alleles from wildspecies [161 162] and use of modern molecular technologieshelping in increasing genetic gain of economic traits In thisscenario it is believed that sequencing of the G raimondii[159] and G arboreum [160] draft genomes will facilitate thegene discovery of important traits These genome resourcescan also be used for discovery of high-throughput markerplatforms like Select SNP arrays These high-throughputDNAmarkers will be helpful in recognizing the cotton geno-types carrying desired characters and was successfully usednot only to study the genetic diversity but to develop linkagemaps and mapping agronomic traits [12 20] which arenecessary for acceleration of varietal development Althoughthe QTL mapping for the various traits that is fiber yieldand quality [131] drought tolerance [133] disease resistance[163 164] and pests resistance [165] have been accomplishedin cotton but these may not be helpful to clone causal genesdue to lower marker densities In general the choice of amolecular marker technique is based on reliability statisticalpower and level of polymorphisms Since their inventionthey are being continuously modified for improved utilityto solve many problems and to bring forth automationWhen these markers techniques reach a greater degree ofautomation then it will be suitable to use DNA markersdirecting to a new ldquoGreen Revolutionrdquo in the agriculturalworld
Presently the enormous development of more efficientDNAmarkers will go on in the future because they can serveas an important tool for the plant breeders and geneticists
to develop the cultivars of cotton that are demanded bythe society It has been proposed that SNPs marker willhave large influence on MAS and mapping studies in futuredue to high abundance and development of sophisticateddetection system [195] GBS will clearly become the markergenotyping platform in coming years So the development ofnovel markers such as GBS and SNPs and the accessibility ofmodern technologies such as DNA Chips and microarrayshasten genome mapping and subsequent gene discovery inthe cotton for efficient cotton varietal development
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgment
We are highly thankful to Dr Awais Rasheed (CIMMYTChina) for his valued inputs and comments
References
[1] USDA Cotton and Wool Year book Dataset 2011 httpusdamannlibcornelleduMannUsdaviewDocumentInfododocu-mentID=128
[2] K F Abdellatif Y A Khidr Y M Mansy M M Lawendey andY A Soliman ldquoMolecular diversity of Egyptian cotton (Gossyp-ium barbadense L) and its relation to varietal developmentrdquoJournal of Crop Science and Biotechnology vol 15 pp 93ndash992012
[3] T Zhang N Qian X Zhu et al ldquoVariations and transmissionof QTL alleles for yield and fiber qualities in upland cottoncultivars developed in Chinardquo PLoS ONE vol 8 no 2 ArticleID e57220 2013
[4] H J Kim and B A Triplett ldquoCotton fiber growth in plantaand in vitro Models for plant cell elongation and cell wallbiogenesisrdquo Plant Physiology vol 127 no 4 pp 1361ndash1366 2001
[5] Y-L Ruan D J Llewellyn and R T Furbank ldquoSuppressionof sucrose synthase gene expression represses cotton fiber cellinitiation elongation and seed developmentrdquo Plant Cell vol 15no 4 pp 952ndash964 2003
[6] Y-M Qin and Y-X Zhu ldquoHow cotton fibers elongate a tale oflinear cell-growth moderdquo Current Opinion in Plant Biology vol14 no 1 pp 106ndash111 2011
[7] P A Fryxell ldquoA revised taxonomic interpretation of GossypiumL (Malvaceae )rdquo Rheedea vol 2 pp 108ndash165 1992
[8] J O Beasley ldquoThe production of polyploids in gossypiumrdquoJournal of Heredity vol 31 no 1 pp 39ndash48 1940
[9] J E Endrizzi E L Turcotte and R J Kohel ldquoGenetics cytologyand evolution of Gossypiumrdquo Advances in Genetics vol 23 pp271ndash375 1985
[10] I Y Abdurakhmonov R J Kohel J Z Yu et al ldquoMoleculardiversity and associationmapping of fiber quality traits in exoticG hirsutum L germplasmrdquo Genomics vol 92 no 6 pp 478ndash487 2008
[11] J F Wendel and R C Cronn ldquoPolyploidy and the evolutionaryhistory of cottonrdquo Advances in Agronomy vol 78 pp 139ndash1862003
10 The Scientific World Journal
[12] Z J Chen B E Scheffler E Dennis et al ldquoToward sequencingcotton (Gossypium) genomesrdquo Plant Physiology vol 145 no 4pp 1303ndash1310 2007
[13] M J Iqbal O U K Reddy K M El-Zik and A E PepperldquoA genetic bottleneck in the lsquoevolution under domesticationrsquoof upland cotton Gossypium hirsutum L examined using DNAfingerprintingrdquoTheoretical and Applied Genetics vol 103 no 4pp 547ndash554 2001
[14] J O Beasley ldquoThe origin of American tetraploid GossypiumspeciesrdquoThe American Naturalist vol 74 pp 285ndash286 1940
[15] J O Beasley ldquoMeiotic chromosome behavior in species specieshybrids haploids and induced polyploids ofGossypiumrdquoGenet-ics vol 27 no 1 pp 25ndash54 1942
[16] J F Wendel C L Brubaker and A E Percival ldquoGeneticdiversity in Gossypium hirsutum and the origin of uplandcottonrdquoAmerican Journal of Botany vol 79 no 11 pp 1291ndash13101992
[17] A M Abdalla O U K Reddy K M El-Zik and A E PepperldquoGenetic diversity and relationships of diploid and tetraploidcottons revealed using AFLPrdquoTheoretical and Applied Geneticsvol 102 no 2-3 pp 222ndash229 2001
[18] X L Song X Z Sun T Z Zhang and H G Wang ldquoAdvanceson genetic diversity of cotton (Gossypium)rdquo Acta BotanicaBoreali-Occidentalia Sinica vol 24 pp 2393ndash2397 2004
[19] Z-S Zhang Y-H XiaoM Luo et al ldquoConstruction of a geneticlinkage map and QTL analysis of fiber-related traits in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 144 no 1-2 pp91ndash99 2005
[20] H-B Zhang Y Li BWang andPWChee ldquoRecent advances incotton genomicsrdquo International Journal of Plant Genomics vol2008 Article ID 742304 20 pages 2008
[21] K Arumuganathan and E D Earle ldquoNuclear DNA contentof some important plant speciesrdquo Plant Molecular BiologyReporter vol 9 no 3 pp 208ndash218 1991
[22] A H Paterson and R H Smith ldquoFuture horizons biotech-nology of cotton improvementrdquo in Cotton Origin HistoryTechnology and Production pp 415ndash432 John Wiley amp SonsNew York NY USA 1999
[23] V Tatineni R G Cantrell and D D Davis ldquoGenetic diversityin elite cotton germplasm determined by morphological char-acteristics and RAPDsrdquo Crop Science vol 36 no 1 pp 186ndash1921996
[24] C L Brubaker and J F Wendel ldquoRFLP diversity in cottonrdquo inGenetic Improvement of Cotton Emerging Technologies pp 81ndash101 Science Publishers Enfield NH USA 2001
[25] N D Young ldquoConstructing a plant genetic linkage map withDNA markersrdquo in DNA-Based Markers in Plants pp 39ndash57 Kluwer Academic Publishers Dordrecht The Netherlands1994
[26] M Agarwal N Shrivastava andH Padh ldquoAdvances inmolecu-lar marker techniques and their applications in plant sciencesrdquoPlant Cell Reports vol 27 no 4 pp 617ndash631 2008
[27] S Preetha and T S Raveendren ldquoMolecular marker technologyin cottonrdquo Biotechnology and Molecular Biology Reviews vol 3no 2 pp 32ndash45 2008
[28] J R Andersen and T Lubberstedt ldquoFunctional markers inplantsrdquo Trends in Plant Science vol 8 no 11 pp 554ndash560 2003
[29] R K Kalia M K Rai S Kalia R Singh and A K DhawanldquoMicrosatellite markers an overview of the recent progress inplantsrdquo Euphytica vol 177 no 3 pp 309ndash334 2011
[30] N Appleby D Edwards and J Batley ldquoNew technologiesfor ultra-high throughput genotyping in plantsrdquo Methods inMolecular Biology vol 513 pp 19ndash39 2009
[31] Q H Xu X L Zhang and Y C Nie ldquoGenetic diversityevaluation of cultivars (G hirsumtum L) from the Changjiangriver valley and Tellow river valley by RAPD markersrdquo ActaGenetica Sinica vol 28 no 7 pp 683ndash690 2001
[32] H J Lu and G O Myers ldquoGenetic relationships and discrim-ination of ten influential upland cotton varieties using RAPDmarkersrdquoTheoretical and Applied Genetics vol 105 no 2-3 pp325ndash331 2002
[33] I Alvarez and J F Wendel ldquoCryptic interspecific introgressionand genetic differentiation within Gossypium aridum (Mal-vaceae) and its relativesrdquo Evolution vol 60 no 3 pp 505ndash5172006
[34] S Liu RGCantrell J CMcCarty Jr and JM Stewart ldquoSimplesequence repeat-based assessment of genetic diversity in cottonrace stock accessionsrdquoCrop Science vol 40 no 5 pp 1459ndash14692000
[35] L F Zhu X L Zhang and Y C Nie ldquoAnalysis of geneticdiversity in upland cotton (Gossypium hirsutum L) cultivarsfrom China and foreign countries by RAPDs and SSRsrdquo Journalof Agricultural Biotechnology vol 11 pp 450ndash455 2003
[36] M P Reddy N Sarla and E A Siddiq ldquoInter simple sequencerepeat (ISSR) polymorphism and its application in plant breed-ingrdquo Euphytica vol 128 no 1 pp 9ndash17 2002
[37] C Schlotterer ldquoThe evolution of molecular markersmdashjust amatter of fashionrdquo Nature Reviews Genetics vol 5 no 1 pp63ndash69 2004
[38] C L Brubaker and J F Wendel ldquoReevaluating the origin ofdomesticated cotton (Gossypium hirsutum Malvaceae) usingnuclear restriction fragment length polymorphisms (RFLPs)rdquoAmerican Journal of Botany vol 81 no 10 pp 1309ndash1326 1994
[39] Z H Yu Y H Park G R Lazo and R J KohelMolecularMap-ping of the Cotton Genome Agron Abstracts ASA MadisonWis USA 1997
[40] C L Brubaker A H Paterson and J F Wendel ldquoComparativegenetic mapping of allotetraploid cotton and its diploid progen-itorsrdquo Genome vol 42 no 2 pp 184ndash203 1999
[41] M Ulloa and W R Meredith Jr ldquoGenetic linkage map andQTL analysis of agronomic and fiber traits in an intraspecificpopulationrdquo Journal of Cotton Science vol 4 no 3 pp 161ndash1702000
[42] M Ulloa W R Meredith Jr Z W Shappley and A L KahlerldquoRFLP genetic linkage maps from four F
23populations and
a joinmap of Gossypium hirsutum Lrdquo Theoretical and AppliedGenetics vol 104 no 2-3 pp 200ndash208 2002
[43] A J Reinisch J-M Dong C L Brubaker D M Stelly J FWendel and A H Paterson ldquoA detailed RFLP map of cottonGossypium hirsutum x Gossypium barbadense chromosomeorganization and evolution in a disomic polyploid genomerdquoGenetics vol 138 no 3 pp 829ndash847 1994
[44] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoD-subgenome bias of Xcm resistance genes in tetraploidGossypium (cotton) suggests that polyploid formation hascreated novel avenues for evolutionrdquo Genetics vol 149 no 4pp 1987ndash1996 1998
[45] H A Erlich PCR Technology Principles and Applications forDNA Amplification W H Freeman New York NY USA 1991
[46] J G KWilliams A R Kubelik K J Livak J A Rafalski and SV Tingey ldquoDNApolymorphisms amplified by arbitrary primers
The Scientific World Journal 11
are useful as geneticmarkersrdquoNucleic Acids Research vol 18 no22 pp 6531ndash6535 1990
[47] S Khanam A Sham J L Bennetzen and M A M Aly ldquoAnal-ysis of molecular marker-based characterization and geneticvariation in date palm (Phoenix Dactylifera L)rdquo AustralianJournal of Crop Science vol 6 no 8 pp 1236ndash1244 2012
[48] K J Chalmers R Waugh J I Sprent A J Simons and WPowell ldquoDetection of genetic variation between and withinpopulations of Gliricidia sepium and G maculata using RAPDmarkersrdquo Heredity vol 69 pp 465ndash472 1992
[49] D S Multani and B R Lyon ldquoGenetic fingerprinting ofAustralian cotton cultivars with RAPD markersrdquo Genome vol38 no 5 pp 1005ndash1008 1995
[50] M KWajahatullah and J M Stewart ldquoGenomic affinity amongGossypium subgenus Sturtia species by RAPD analysisrdquo inProceeding of the Beltwide Cotton Conference National CottonCouncil p 452 Memphis Tenn USA 1997
[51] C D Geng Z Z Gong J Q Huang and Z C ZhangldquoIdentification of difference between cotton cultivars (G hirsu-tum) using the RAPD methodrdquo Jiangsu Journal of AgriculturalSciences vol 11 no 4 pp 21ndash24 1995
[52] T H Lan C G Cook and A H Paterson ldquoIdentification of aRAPDmarker linked tomale fertility restoration gene in cotton(Gossypium hirsutum L)rdquo Journal of Agricultural Genomics vol1 pp 1ndash5 1999
[53] B Shu K Fenling Z Y Yao Z G Mei Z Q Yuan and W XGang ldquoGenetic diversity analysis of representative elite cottonvarieties in three main cotton regions in China by RAPD andits relation with agronomic characteristicsrdquo Scientia AgriculturaSinica vol 34 pp 597ndash603 2001
[54] M Ulloa R G Cantrell R G Percy E Zeiger and Z Lu ldquoQTLanalysis of stomatal conductance and relationship to lint yieldin an interspecific cottonrdquo Journal of Cotton Science vol 4 no1 pp 10ndash18 2000
[55] B Bornet and M Branchard ldquoNonanchored inter simplesequence repeat (ISSR)markers reproducible and specific toolsfor genome fingerprintingrdquo Plant Molecular Biology Reportervol 19 no 3 pp 209ndash215 2001
[56] T M Culley and A D Wolfe ldquoPopulation genetic structureof the cleistogamous plant species Viola pubescens Aiton (Vio-laceae) as indicated by allozyme and ISSR molecular markersrdquoHeredity vol 86 no 5 pp 545ndash556 2000
[57] J B Wang ldquoISSR markers and their applications in plantgeneticsrdquo Yi Chuan vol 24 no 5 pp 613ndash616 2002
[58] T Nagaoka and Y Ogihara ldquoApplicability of inter-simplesequence repeat polymorphisms inwheat for use asDNAmark-ers in comparison to RFLP and RAPDmarkersrdquoTheoretical andApplied Genetics vol 94 no 5 pp 597ndash602 1997
[59] M Z Galvan B Bornet P A Balatti and M BranchardldquoInter simple sequence repeat (ISSR) markers as a tool for theassessment of both genetic diversity and gene pool origin incommon bean (Phaseolus vulgaris L)rdquo Euphytica vol 132 no3 pp 297ndash301 2003
[60] A Shi S Kantartzi M Mmbaga and P Chen ldquoDevelopmentof ISSR PCR markers for diversity study in dogwood (Cornusspp)rdquo Agriculture and Biology Journal of North America vol 1pp 189ndash194 2010
[61] M W Blair O Panaud and S R McCouch ldquoInter-simplesequence repeat (ISSR) amplification for analysis of microsatel-litemotif frequency and fingerprinting in rice (Oryza sativa L)rdquoTheoretical and Applied Genetics vol 98 no 5 pp 780ndash7921999
[62] B Bornet C Muller F Paulus and M Branchard ldquoHighlyinformative nature of inter simple sequence repeat (ISSR)sequences amplified using tri- and tetra-nucleotide primersfrom DNA of cauliflower (Brassica oleracea var botrytis L)rdquoGenome vol 45 no 5 pp 890ndash896 2002
[63] M Sica G Gamba S Montieri L Gaudio and S AcetoldquoISSR markers show differentiation among Italian populationsofAsparagus acutifolius Lrdquo BMCGenetics vol 6 article 17 2005
[64] P Vos R Hogers M Bleeker et al ldquoAFLP a new technique forDNA fingerprintingrdquo Nucleic Acids Research vol 23 no 21 pp4407ndash4414 1995
[65] G O Myers B Jiang M W Akash A Badigannavar and SSaha ldquoChromosomal assignment of AFLP markers in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 165 no 2 pp391ndash399 2009
[66] K Lukonge L Hersalman and M T Labuschagne ldquoGeneticdiversity of tanzanian cotton revealed by AFLP analysisrdquo inProceedings of the African Crop Science Conference vol 8 pp773ndash776 2007
[67] N Murtaza ldquoCotton genetic diversity study by AFLP markersrdquoElectronic Journal of Biotechnology vol 9 no 4 pp 456ndash4602006
[68] M Zhong J CMcCarty J N Jenkins and S Saha ldquoAssessmentof day-neutral backcross populations of cotton using AFLPmarkersrdquo Journal of Cotton Science vol 6 no 2 pp 97ndash1032002
[69] A Rakshit S Rakshit J Singh et al ldquoAssociation of AFLPand SSR markers with agronomic and fibre quality traits inGossypium hirsutum Lrdquo Journal of Genetics vol 89 no 2 pp155ndash162 2010
[70] A Badigannavar and G Myers ldquoGenetic analysis of AFLPmarkers associated with seed quality traits in upland cotton(Gossypium hirsutum)rdquo in Beltwide Cotton Conferences NewOrleans La USA 2010
[71] M K Altaf J M C D Stewart M K Wajahatullah J Zhangand R G Cantrell ldquoMolecular and morphological geneticsof a trispecies F2 population of cottonrdquo in Proceedings of theBeltwide Cotton Conferences vol 1 pp 448ndash452 New OrleansLa USA January 1997
[72] M K Rana and K V Bhat ldquoA comparison of AFLP andRAPD markers for genetic diversity and cultivar identificationin cottonrdquo Journal of Plant Biochemistry and Biotechnology vol13 no 1 pp 19ndash24 2004
[73] J-M Lacape T-B Nguyen S Thibivilliers et al ldquoA combinedRFLP-SSR-AFLP map of tetraploid cotton based on a Gossyp-ium hirsutum times Gossypium barbadense backcross populationrdquoGenome vol 46 no 4 pp 612ndash626 2003
[74] D TautzM Trick andG A Dover ldquoCryptic simplicity in DNAis amajor source of genetic variationrdquoNature vol 322 no 6080pp 652ndash656 1986
[75] S Saha J Wu J N Jenkins et al ldquoBreeding and genetics effectof chromosome substitutions from Gossypium barbadense L 3-79 into G hirsutum L TM-1 on agronomic and fiber traitsrdquoJournal of Cotton Science vol 8 no 3 pp 162ndash169 2004
[76] O U K Reddy A E Pepper I Abdurakhmonov et al ldquoNewdinucleotide and trinucleotide microsatellite marker resourcesfor cotton genome researchrdquo Journal of Cotton Science vol 5no 2 pp 103ndash113 2001
[77] T B Nguyen M Giband P Brottier A M Risterucci and JM Lascape ldquoWide coverage of the tetraploid cotton genomeusing newly developed microsatellite markersrdquoTheoretical andApplied Genetics vol 109 no 1 pp 167ndash175 2004
12 The Scientific World Journal
[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
4 The Scientific World Journal
RFLP and PCR [87] in which DNA fragments are ampli-fied through PCR followed by digestion with a restrictionenzyme [88] Subsequently polymorphisms arise from thevariation in the incidence of restriction sites of identi-fied alleles are detected by gel electrophoresis [88] CAPSmicrosatellite and CAPS are technically alike and use ofmicrosatellite spheres and flanking regions as a templatemay have a decisive improvement over the well-known DNAmarkers in crop species CAPS microsatellites change themonomorphic markers into polymorphic markers whichmostly inherited in codominant way [89] and exhibit highpolymorphism between strongly related genotypes Any basesubstitutions can be identified by CAPS microsatellites as thepolymorphism exhibited by this technique is based on thesequence dissimilarities in the flanking regions aside fromthe microsatellite spheres These markers also assist in theanalysis of composite traits by genemapping and propose theopportunity of identifying markers by physiological and bio-chemical characteristics of their gene products [86]Howeverthe CAPSmarkers are only developedwheremutations createa recognition site for restriction enzyme [87]
23 Sequence Based DNAMarkers
231 Single Nucleotide Polymorphism Variations of singlenucleotide (A T C G) in sequence of individual genomeare known as single nucleotide polymorphism or SNPs [26]These may occur in the noncoding coding and intergenicregions of the genome so allowing the detection of the genesdue to the variations in the sequences of nucleotides [26 90]and these are either nonsynonymous or synonymous withinthe coding regions of the genome Synonymous changes canalter mRNA splicing that result the changes in the phenotypeof an individual [91]
SNP markers are important tool for linkage mappingmap based cloning and marker assisted selection due to thehigh level of polymorphismThe codominant nature of SNPsmakes thesemarkers able to distinguish the heterozygous andhomozygous alleles [92] Narrow genetic base and allotetrap-loid genome has made the discovery of SNPs difficult incotton [93] Recently use of high throughput sequencingtechniques have made it possible to detect great numbersof SNP markers [94 95] including organisms with limitedmolecular studies [96 97] and organisms with slight geneticvariation such as cotton [85] In cotton many researcheshave been conducted to observe diversity characteriza-tion and mapping of SNPs in the nucleotide sequenceof Gossypium genome [98 99] Recently an internationalcollaborative effort has developed 70K SNP chip basedon Illumina Infinium genotyping assay (Unpublished datahttpwwwcottongenorgnode1287616)This high-through-put genotyping assay will be a resource that will be usedglobally by public and private breeders geneticists and otherresearchers to enhance cotton genetic analysis breedinggenome sequence assembly and many other uses SimilarlyGene Chip cotton genome array comprising of 239777 probesets representing 21485 cotton transcripts has been developedand under validation step before commercially available by
Affymetrix (httpwwwaffymetrixcomproducts servicesarraysspecificcottonaffx)The sequences used for SNP chipdevelopment were selected from GenBank dbEST and Ref-Seq contributed by the collaborators globally These high-throughput technologies will be helpful for fine mapping andsubsequent gene discovery for important economic traits incotton Additionally these resources will provide foundationsto initiate genomic selection studies in cotton ultimatelyenhancing genetic gain from breeding
232 Genotyping by Sequencing GBS Genotyping-by-se-quencing (GBS) is a technique that simultaneously detectsand genotypes the SNPs in a genome [100] GBS was devel-oped as a simple but strong access for reducing complexityin complex genomes [101] The development of the GBSlibrary is very simpleThe original GBS method used a singlerestriction enzyme to capture the genomic sequence betweenrestriction sites [101]
The choice of restriction enzyme is a crucial factor inGBS for covering the repetitive regions in the genomesIn the original GBS approach used in maize and barleyone restriction enzyme (RE) ldquoApeKIrdquo was used which ismethylation-sensitive to reduce the complexity of the genomeand to choose hypomethylated sphere of the genome forsequencing [101] A modified GBS approach was also devel-oped in which two enzymes and a Y-adapter were usedto generate ldquouniformrdquo GBS libraries where Adapter 1 andAdapter 2were on opposite ends of every fragment [102] GBSis a multiple approach that can discover thousands of SNPs inan experiment and suitable for population studies genomicselection genetic mapping germplasm characterization andother breeding applications in different organisms [101ndash103]GBS technique can also be employed in species of plants thatdo not have available reference genome In these cases thesequence tags can be deal as dominant markers for analysis[100]
3 Overview of Marker Based CropImprovement Efforts
31 Genetic Diversity in Cotton The success of any breedingprogram mainly depends on the availability of the geneticdiversity in the germplasm resources Understanding of thegenetic relationships among plant genotypes is significantto know the complexity of available germplasm to discoverthe differences in available genotypes and to build up usefulconservation plans [104] Thus evaluation based on themolecular markers can give valuable insight into the geneticstructure of a plant population which helps in the devel-opment of new varieties [105] The genetic diversity studiesin cotton germplasm using different marker technologies aresummarized in Table 2 A narrow genetic base is reported incotton by several workers using different molecular markers[23 38 49 106 107]
RAPD and ISSR techniques have been utilized to analyzegenetic diversity and hybridization and for the incident ofsomaclonal variations in various crops involving cotton [108ndash112] Five prominent studies were conducted to evaluate
The Scientific World Journal 5
Table2Anoverview
ofgenetic
diversity
studies
incotto
nusingmolecular
markers
Marker
Cou
ntry
Popu
latio
ntype
Size
References
RAPD
s
USA
16near-hom
ozygou
selitec
ottongeno
types
80RA
PDprim
ers
[23]
Pakista
n31
Gossypium
species3subspecies
and1interspecifich
ybrid
45RA
PDprim
ers
[115]
USA
10varie
tieso
fUplandcotto
n86
RAPD
prim
ers
[32]
Pakista
n30
cultivarsof
Garboretum
50RA
PDprim
ers
[169]
Iran
13F 1
andF 2
cotto
ngeno
types(Gossypium
hirsutum
)obtainedby
crossin
g30
RAPD
prim
ers
[170]
India
Intraspecific
cotto
nF 1
hybrid
andits
parents
20RA
PDprim
ers
[171]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
40RA
PDprim
ers
[172]
SSRs
USA
24cultivarsof
Ghirsutum
88SSRprim
ers
[173]
China
39accessions
ofG
arboreum
358SSRprim
ers
[174]
China
108accessions
ofAs
iatic
cotto
nand1G
herbaceum
60SSRprim
ers
[175]
China
43sourceso
fUplandcotto
ngerm
plasm
36SSRprim
ers
[124]
France
47geno
typeso
ftetraploidcotto
n320SSRprim
ers
[176]
USA
96accessions
ofG
arboreum
115Genom
icandES
T-SSRs
[177]
Pakistan
8accessions
ofG
hirsutum
32SSRprim
ers
[178]
China
59geno
typeso
fGhirsutum
40ES
T-SSRprim
ers
[179]
Greece
29geno
typeso
fGhirsutum
andan
interspecific
hybrid
12SSRprim
erpairs
[180]
China
56accessions
ofSeaisla
ndcotto
n237SSRprim
ers
[125]
Egypt
28geno
typeso
fEgyptiancotto
n6SSRand5ES
T-SSRprim
er[2]
Pakista
n19
geno
typeso
fBtcotton
104SSRprim
ers
[107]
USA
193cultivarsof
Uplandcotto
n44
8SSRprim
ers
[126]
USA
378accessions
ofG
hirsutum
and3of
Gbarbadense
120SSRprim
ers
[181]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
4SSRprim
ers
[172]
AFL
Ps
USA
11accessions
ofG
hirsutum
and2fro
meach
ofG
arboreum
Gherbaceum
andG
barbadense
4EcoR
I-MseIp
rimersfor
AFL
P[106]
Belgium
Uplandcotto
nwild
species(G
raim
ondiiand
Gthurbrii)
andtheirB
C 3progenies
5AFL
Pprim
ers
[117]
USA
3diploidspecieso
fGossypium
3G
barbadensecultivarsand43
Ghirsutum
accessions
20AFL
Pprim
ers
[13]
USA
29accessions
from
fives
pecies
oftheg
enus
Gossypium
16AFL
Pprim
ers
[17]
India
24lin
esof
Ghirsutum
L6AFL
Pprim
ers
[182]
Norway
131a
ccessio
nsof
Gbarbadan
se8AFL
Pprim
ers
[183]
ISSR
s
Iran
13F 1
andF 2
cotto
ngeno
types(Gossypium
hirsutum
)8ISSR
prim
ers
[170]
Egypt
28Eg
yptia
ncotto
ngeno
types
5ISSR
prim
ers
[2]
India
Intraspecific
cotto
nF 1
hybrid
andits
parents
19ISSR
prim
ers
[171]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
20ISSR
prim
ers
[172]
SNPs
Pakista
n2cultivarsof
tetraploid
cotto
nPrim
ersc
orrespon
dto
FIF1
gene
[184]
USA
24lin
esof
cotto
n270SN
Plociand92
Indel
[99]
6 The Scientific World Journal
genetic diversity using RAPD markers during 90s Geneticdiversity of 16 elite homozygous genotypes obtained fromthe inter-specific hybridization was studied using 80 RAPDmarkers [23] RAPD markers were used to differentiate theG hirsutum lines from the G arboretum [113] Similarly25 short duration genotypes of cotton were analyzed usingarbitrary primers [114] Later [115] studied genetic diversityof 31 Gossypium species 3 subspecies and 1 interspecifichybrid using 45 RAPD primers and the results showed thatgenetic relationship of many species is related to the centerof origin Recently genetic diversity in 18 cotton genotypes ofPakistan studied by 5 RAPD primers showed that two diversegenotypes of cotton (CIM-240 and CIM-443) have resistanceagainst cotton leaf curl virus [116]
AFLP technique was also used to distinguish the dif-ferences among diploid and tetraploid species of cotton byutilizing the variations in ribosomal RNA genes [106] Thegenetic diversity between the upland cotton wild species (Graimondii G thurberii and G sturtianum) and their BC
3
progenies was evaluated usingAFLPmarkers [117] Intra- andinterspecific relatedness of theG barbadense G arboreumGraimondii and G hirsutum are determined by AFLPs whichdemonstrated its usefulness for genetic relatedness acrosswide range of species [17] The relationship between the par-ents and four day neutral backcross generations of cotton wasdetermined using 43 AFLP markers [68] Comparative studywas conducted to evaluate AFLP and RAPD techniques using16 diploid cotton genotypes and it was concluded that AFLPmarkers are more efficient for polymorphism detection andfor analyzing of genetic diversity as compared to RAPDs [72]Similarly genetic diversity of 26 Tanzanian cotton genotypes(Gossypiumhirsutum L) was studied using theAFLPmarkers[66] The results of this study indicated the high values ofgenetic similarity which show the lower genetic diversityamong Tanzanian cotton cultivars Reference [65] mapped98 AFLP markers and assigned 22 distinctive chromoso-mal positions using cytogenetic deletion stocks Mappinginformation enhanced the utilization of AFLPs and can beused to saturate the existing marker frequency over differentchromosomes
In cotton SSRs are considered as a new class of DNAmarkers which hastened cotton genetic diversity and map-ping studies [27] and are important source to observe thetranscribed genes [118] There are multiple reports aboutusing the SSR markers for genetic diversity Reference [119]identified 71 SSR loci with 65 primer pairs and placed themondistinctive chromosomes of cotton Genetic diversity amongUS and Australian cultivars and day neutral lines of Ghirsutum was also analyzed by SSR markers [120]
Further saturation of SSR markers was extended by addi-tion of 204 markers which exhibited 261 segregating bandsgiving rise to 233 mapped loci in cotton [77] Interspecificpolymorphism between G barbadense and G hirsutum wasalso studied using SSR markers and results showed thatpolymorphism between species was high but it was lowwithin species [121] Reference [122] developed new SSRmarkers analyzed the status of 23 chromosomes and foundthat the inter loci distance was 49 cM Diversity among52 different G hirsutum cultivars was studied by 31 SSR
primer pairs and successfully discriminated the 52 cultivarsthrough broader allelic coverage [123] Similarly geneticdiversity of 43 upland cotton varieties [124] 56 sea-islandcotton accessions [125] 19 Bt cotton genotypes [107] 50representative Pakistani genotypes [104] and 193 uplandcotton cultivars [126] were evaluated using 36 237 104 70and 448 SSR markers respectively SSRs have also been usedto assess the genetic purity of the cotton hybrids [127] anddemonstrated as an effective tool for hybrid identification
Recent developments in next generation sequencing(NGS) and RNA-seq technology have generated high-throughput sequence data which facilitated the identificationof SNPs as effective and highly saturated markers for geneticstudies in cotton Genetic variations within and betweenthe different species of cotton have been characterized by1000 SNPs and 279 In-Dels from the 270 and 92 locisegregating in G barbadense and G hirsutum to providemapped molecular markers for crosses within species andintrogression of foreign germplasm in cotton [99] A genomereduction experiment based on the restriction site conserva-tion (GR-RSC) and previously generated assembly of expresssequence tags (ESTs) were used to discover the SNPs in 4accessions of G hirsutum and G barbadense A total 11834and 1679 non-genic and 4327 genic SNPs were identified inthe GR-RSC and EST assemblies using highly conservationparameters The KASPer assays were used to target the 1052(704 nongenic and 348 genic) genome specific SNPs betweenthe G hirsutum accessions [93] The assay then tested forthe Mendelian segregation ratio in the F
2population derived
from a cross of upland cotton (G hirsutum) cultivars
32 QTLs Mapping for Important Economic Traits in Cot-ton The regions in genomes to have genes linked with aquantitative trait are known as quantitative trait loci QTLs[128] and the process of developing linkage maps andperforming QTL analysis is referred to as QTLmapping [129130] QTL analysis stands on the principal of identifying aconnection among phenotype and genotype ofmarkers [128]The QTLs identified in cotton germplasm using differentmarker technologies are summarized in Table 3
RFLPs have been widely used to map genes of economicinterest in cotton Previously RFLP map of G hirsutum andG barbadensewas used tomap 14QTLs for fiber related traits[131] Similarly genes influencing density of stem and leaftrichomes [132] high gossypol plant and low seed gossypolcontents [117] were confined by RFLP markers Reference[131] developed an RFLP map of 261 markers distributedamong 26 linkage groups using F
2plants from an interspecific
cross Another genetic linkage map was developed usingRFLP markers and 26 QTLs were recognized for agronomicand fiber quality traits [41] Later on RFLP based QTLmapping was extended to leaf chlorophyll contents [133]Backcross population of G hirsutum and G barbadense wasused to map 28 9 and 8 QTLs for fiber length lengthuniformity and short fiber contents respectively using the262 RFLP markers [134]
RAPDs have also been widely used for QTL mappingin cotton however lack of reproducibility and unknown
The Scientific World Journal 7
Table3Anoverview
ofQTL
studies
incotto
n
Traits
Descriptor
Popu
latio
nSize
Marker(nu
mbera
ndtype)
QTL
snum
ber
Reference
Fiberq
uality
FSFLandFF
F 2171
RFLP
sand
85RA
PDs
13[135]
FSF 2
186
217SSRs800
RAPD
sUBC
and1040
OPE
RON
2[153]
LYLPSW
NSUQSFFL
FE
FTFFandIF
F 2120
144AFL
PsR
FLPs
and150SSRs
28[14
1]FS
FE
FLFU
LPandFF
F 2117
290SSRs
and9AFL
Ps16
[19]
FFBC
3F2
3662
262RF
LPs
41[185]
FLFLU
andSFC
BC3F
23662
262RF
LPs
45[134]
FSFE
FUFLandFF
RILrsquos
270
7508
SSRs384
SRAPs
and740IT-ISJs
13[186]
FLFSFF
andFE
F 2mdash
1378
SSRs
39[136]
FSFLFFFMTFE
andSFI
RILrsquos
180
4106
SSRsA
FLPsR
APD
sand
SRAPs
48[187]
FEFLFS
FFandFU
CP172
16052SSRs
63[188]
Fibera
ndagrono
mical
SCYLYLPBW
SIFM
TPE
RWFWTFFFLFE
andFS
RILrsquos
188
141S
SRs
56[189]
Yield
andfib
er
FSFLFFFE
LPSINB
SCYandLY
RILrsquos
258
2131
SSRs
53[19
0]
NB
BWSILPLISC
YLYFLFS
FFFE
andFU
4WCandinbred
lines
280
6123
SSRs
andES
T-SSRs
31[138]
SCYLYN
BBW
LPSILIand
FBN
RILrsquos
andIF2
180
2675
EST-SSRs
111
[191]
PHFBN
BWLPLISILYFLFS
FE
FFandFU
Ghirsutum
accessions
81121S
SRs
180
[3]
LISILYSCY
NSB
andFS
F 269
834SSRs437
SRAPs107
RAPD
sand
16RE
MAPs
52[192]
Morph
ological
LBNOSL1L1W1L2
W2L3
andW3
F 2180
261R
FLPs
62[19
3]EM
F 2andF 3
mdash40
83SSRs
54[14
0]NFB
F 2251
1165SSRs
5[19
4]Plant
architectural
PHFBL
FBN
FBA
FBL
PHandNMUB
RILrsquos
180
2130
SSRs2
RAPD
sand
1SRA
P16
[137]
NB
numbero
fbollsperp
lantB
Wb
ollw
eightSIseedindexLP
lintp
ercentL
Ilin
tind
exSIseed
indexSC
Yseed
cotto
nyieldperp
lantLY
linty
ield
perp
lantF
Lfib
erleng
thF
Sfib
erstr
ength
FEfi
ber
elong
ation
FUfiberu
niform
ityratio
FY
fiber
yello
wnessFFfib
erfin
enessFM
Tfib
ermaturityP
Hplant
heightFBL
fruitbranch
leng
thFBN
fruitbranch
numberFB
Afruitbranch
angleFL
Ufiberlength
unifo
rmitySFC
sho
rtfib
ercontentFR
fiberreflectanceSW
seedweightNSnu
mbero
fseeds
perp
lantU
Qupp
erqu
artilelengthSFsho
rtfib
ercontentFT
fibertenacityIFim
maturefi
bercon
tentSFIsho
rtfib
erindexNSB
num
bero
fseeds
perb
ollEM
earlymaturityN
MUB
lowerm
iddleandup
sideb
olln
umberNFB
nod
etofirstfruitin
gbranchLBN
Olob
enum
bersSL1sub
lobe
numbero
nthem
ainlobeL1
main-lobe
leng
thW
1main-lobe
widthL2second
-lobe
leng
thW
2second
-lobe
widthL3third
-lobe
leng
thW
3third
-lobe
leng
thPER
perim
eterW
Fweightfi
tnessWT
wallthicknessFBL
PHratioof
fruit
branch
leng
thto
planth
eightRILrsquosrecom
binant
inbred
linesIF2immortalized
F2s4W
Cfour
way
crossCP
com
positec
rossand
BC3F
2=backcrossfam
ilies
8 The Scientific World Journal
chromosomal positions remained main disadvantages whichrestricted the use of RAPDs in advanced studies Refer-ence [135] used 85 RAPD markers and identified 13 QTLsassociated to the fiber quality in the F
2population derived
from the G hirsutum and G barbadense cross There arenumerous studies on using the RAPDs for QTL mappingalong with other molecular markers (Table 3) An extensiveSSR genotyping was conducted over F
2populations from 3
diverse upland cotton genotypes using 1378 markers and 39fiber related QTLs were identified [136] Recombinant inbredlines (RILs) are also important mapping populations andseveral QTLs related to plant architecture [137] yield [3] andfiber quality [19] have been identified in upland cotton usingRILs About 31QTLs linked to the yield and fiber quality traitsare detected bywide array of SSR and EST SSRmarkers (6123)in 4 way cross populations developed from the 4 inbred linesof G hirsutum [138] A genetic linkage map of the tetraploidcotton was developed using 1601 pairs of SSR and 247 SNPmarkers [139] The genetic map consisted of the 2072 locicovering 3380 cm of the cotton genome Two F
2populations
were generated by the crosses of upland cotton cultivars and4083 SSR markers were used for QTL analysis which detect54 QTLs linked to early maturity [140]
A total of 144 primer combinations of AFLPs and 150 ofSSRs were used to detect 28 QTLs related to the fiber traits[141] To know the significant threshold for the LR statisticspermutation tests were carried out afterwhich 7QTLs remainsignificant RIL lines developed from the intraspecific cross ofupland cotton are used to detect the 12 epistatic and 4 mainQTLs related to the plant architectural traits by 2130 SSR 2RAPD and 1 SRAP markers [137]
Conclusively huge arrays of QTLs have been identifiedusing multiple molecular marker technologies Descriptionof stable QTL from diverse generations common QTL fromvarious populations and homologous QTLs raises the infor-mation on the genetic base Information about distributionof important QTLs in the genome of cotton is very importantand promises the future strategy for marker assisted breed-ing Cotton Gen serves as an important database for suchinformation and currently this database has 988 QTLs for25 different traits (httpwwwcottongenorgdataqtl) whichcan be surveyed according to objectivity
33 Genome Wide Association Studies (GWAS) in CottonAssociation mapping also known as linkage disequilibrium(LD) mapping has appeared as a tool to determine thevariation in complex traits using historical and evolutionaryrecombination actions at the population level [142] In asso-ciation mapping nonstructured populations are phenotypedand genotyped to identify the trait associated with marker[143] This results into capture of wider recombination andhigher resolution mapping as compared to linkage mapping[144] The applications of association mapping for cottonassist extensive employment of natural genetic diversity con-served within the worldwide collections of cotton germplasm[145] as in other plant germplasm resources Turning theefforts of gene-tagging from biparental QTL mapping to LD-based association study promise the productive employment
of ex situ conserved genetic diversity of global germplasmresources of cotton [10] The cotton genome may need fewnumbers of markers for productive associating mappingof complex traits which is also reported for other crops[146] Regarding the tetraploid genome of cotton with atotal recombination length of about 5200 cm and an average400 kb per cm [22] the LD block sizes of sim5-6 cm distanceis sufficient to conduct an association mapping of differenttraits that would require a maximum of sim1000 polymorphicmarkers for successful and reliable associationmapping [147]Extent of genome-wide LD and association mapping offiber quality traits were reported using 95 SSR markers in285 exotic accessions of G hirsutum comprised of 208 lan-draces and 77 varieties [10] Similarly LD-based associationmapping was conducted for fiber quality traits in 335 Ghirsutum germplasm using 202 SSR markers [147] Progressin genome sequencing technology provides an opportunity toproduce large size genotypic data which supports associationmapping over QTL mapping and because of this associationmapping is becoming more common [148]
34 Marker Assisted Selection (MAS) in Cotton Markerassisted selection (MAS) is a procedure by which a phenotypeis selected on the basis of genotype of a marker [128]Selecting the plants in the segregating population that havethe suitable genes combinations is the important componentof plant breeding [149] Once the markers tightly linked tothe genes have been detected breeders may use particularDNA marker to identify the plants carry the genes [150]The effectiveness and cost of MAS are influenced by themarker technique therefore it must be selected carefully[151] During the past two decades RAPDs techniqueshave been used for MAS for getting the glanded plantsand glandless seeds in the interspecific population of Gsturtianum and other species [152] It was exposed that DNAmarkers connected to the major QTL (QTLFS1) for fiberstrength could be utilized inMAS to increase fiber strength ofcommercial varieties in segregating populations [153] SomeRAPD markers were developed into locus specific sequencecharacterized amplified region (SCAR) markers to screen theBC1F4upland cotton For example SCAR 1920marker for the
major fiber strength QTL was developed and has been usedfor selecting desirable genotypes [154] Screening of the SNPswhich aremapped on chromosome 10 recognized extra 3 SNPmarkers thatwere associatedwith blue disease resistance gene(Cbd) which were employed to efficiently characterize a traitallowing MAS for strong levels of blue disease resistance incotton breeding programs [155]
4 Cotton Draft Genome and Its Implication
The increasing information of DNA sequencing allows thediscovery of genes and molecular markers associated withdifferent traits opening new avenues for crop improvement[148] Sequencing of DNA promises to display the spectrumof diversity in the genus Gossypium The tetraploid cottonspecies (2119899 = 4119909 = 52) such as G hirsutum and G bar-
The Scientific World Journal 9
badense are thought to have developed by an allopoly-ploidization that happened nearly 1-2 million years ago inwhich a D-genome species is pollen parent and species of anA-genome is maternal parent [12 156] It is essential to havea basic awareness of the structure of the component genomesto understand the cultivated polyploid genomes their evo-lution and interaction between their subgenomes Towardthe long-term aim of characterizing the diversity amongcotton genomes the cotton geneticists have prioritized the Dgenome progenitor G raimondii for complete sequencing Graimondii has a sim880Mb genome [157] the smallest genomein the genus Gossypium at sim60 of the size of diploid A-genome and 40 of the tetraploids [158] A physical map ofG raimondii genome was assembled and several evidencesreferred that the G raimondii genome is composed of twodifferent qualitative components one that is gene-rich andanother that is repeat-rich [158] About 40976 protein codinggenes and 2355 syntenic blocks identified in the genome ofG raimondii [159] Similarly the sequencing and assemblingof G arboreum genome depicted that 685 of the genomeis covered by repetitive DNA sequences and about 41330protein-coding genes were predicted in the genome of Garboreum [160]
5 Future Prospects
Cotton is a major source of foreign exchange for manycountries around the globe therefore major focus remainsthe enhancement of yield and quality of fiber This challengecan be accomplished by introducing new alleles from wildspecies [161 162] and use of modern molecular technologieshelping in increasing genetic gain of economic traits In thisscenario it is believed that sequencing of the G raimondii[159] and G arboreum [160] draft genomes will facilitate thegene discovery of important traits These genome resourcescan also be used for discovery of high-throughput markerplatforms like Select SNP arrays These high-throughputDNAmarkers will be helpful in recognizing the cotton geno-types carrying desired characters and was successfully usednot only to study the genetic diversity but to develop linkagemaps and mapping agronomic traits [12 20] which arenecessary for acceleration of varietal development Althoughthe QTL mapping for the various traits that is fiber yieldand quality [131] drought tolerance [133] disease resistance[163 164] and pests resistance [165] have been accomplishedin cotton but these may not be helpful to clone causal genesdue to lower marker densities In general the choice of amolecular marker technique is based on reliability statisticalpower and level of polymorphisms Since their inventionthey are being continuously modified for improved utilityto solve many problems and to bring forth automationWhen these markers techniques reach a greater degree ofautomation then it will be suitable to use DNA markersdirecting to a new ldquoGreen Revolutionrdquo in the agriculturalworld
Presently the enormous development of more efficientDNAmarkers will go on in the future because they can serveas an important tool for the plant breeders and geneticists
to develop the cultivars of cotton that are demanded bythe society It has been proposed that SNPs marker willhave large influence on MAS and mapping studies in futuredue to high abundance and development of sophisticateddetection system [195] GBS will clearly become the markergenotyping platform in coming years So the development ofnovel markers such as GBS and SNPs and the accessibility ofmodern technologies such as DNA Chips and microarrayshasten genome mapping and subsequent gene discovery inthe cotton for efficient cotton varietal development
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgment
We are highly thankful to Dr Awais Rasheed (CIMMYTChina) for his valued inputs and comments
References
[1] USDA Cotton and Wool Year book Dataset 2011 httpusdamannlibcornelleduMannUsdaviewDocumentInfododocu-mentID=128
[2] K F Abdellatif Y A Khidr Y M Mansy M M Lawendey andY A Soliman ldquoMolecular diversity of Egyptian cotton (Gossyp-ium barbadense L) and its relation to varietal developmentrdquoJournal of Crop Science and Biotechnology vol 15 pp 93ndash992012
[3] T Zhang N Qian X Zhu et al ldquoVariations and transmissionof QTL alleles for yield and fiber qualities in upland cottoncultivars developed in Chinardquo PLoS ONE vol 8 no 2 ArticleID e57220 2013
[4] H J Kim and B A Triplett ldquoCotton fiber growth in plantaand in vitro Models for plant cell elongation and cell wallbiogenesisrdquo Plant Physiology vol 127 no 4 pp 1361ndash1366 2001
[5] Y-L Ruan D J Llewellyn and R T Furbank ldquoSuppressionof sucrose synthase gene expression represses cotton fiber cellinitiation elongation and seed developmentrdquo Plant Cell vol 15no 4 pp 952ndash964 2003
[6] Y-M Qin and Y-X Zhu ldquoHow cotton fibers elongate a tale oflinear cell-growth moderdquo Current Opinion in Plant Biology vol14 no 1 pp 106ndash111 2011
[7] P A Fryxell ldquoA revised taxonomic interpretation of GossypiumL (Malvaceae )rdquo Rheedea vol 2 pp 108ndash165 1992
[8] J O Beasley ldquoThe production of polyploids in gossypiumrdquoJournal of Heredity vol 31 no 1 pp 39ndash48 1940
[9] J E Endrizzi E L Turcotte and R J Kohel ldquoGenetics cytologyand evolution of Gossypiumrdquo Advances in Genetics vol 23 pp271ndash375 1985
[10] I Y Abdurakhmonov R J Kohel J Z Yu et al ldquoMoleculardiversity and associationmapping of fiber quality traits in exoticG hirsutum L germplasmrdquo Genomics vol 92 no 6 pp 478ndash487 2008
[11] J F Wendel and R C Cronn ldquoPolyploidy and the evolutionaryhistory of cottonrdquo Advances in Agronomy vol 78 pp 139ndash1862003
10 The Scientific World Journal
[12] Z J Chen B E Scheffler E Dennis et al ldquoToward sequencingcotton (Gossypium) genomesrdquo Plant Physiology vol 145 no 4pp 1303ndash1310 2007
[13] M J Iqbal O U K Reddy K M El-Zik and A E PepperldquoA genetic bottleneck in the lsquoevolution under domesticationrsquoof upland cotton Gossypium hirsutum L examined using DNAfingerprintingrdquoTheoretical and Applied Genetics vol 103 no 4pp 547ndash554 2001
[14] J O Beasley ldquoThe origin of American tetraploid GossypiumspeciesrdquoThe American Naturalist vol 74 pp 285ndash286 1940
[15] J O Beasley ldquoMeiotic chromosome behavior in species specieshybrids haploids and induced polyploids ofGossypiumrdquoGenet-ics vol 27 no 1 pp 25ndash54 1942
[16] J F Wendel C L Brubaker and A E Percival ldquoGeneticdiversity in Gossypium hirsutum and the origin of uplandcottonrdquoAmerican Journal of Botany vol 79 no 11 pp 1291ndash13101992
[17] A M Abdalla O U K Reddy K M El-Zik and A E PepperldquoGenetic diversity and relationships of diploid and tetraploidcottons revealed using AFLPrdquoTheoretical and Applied Geneticsvol 102 no 2-3 pp 222ndash229 2001
[18] X L Song X Z Sun T Z Zhang and H G Wang ldquoAdvanceson genetic diversity of cotton (Gossypium)rdquo Acta BotanicaBoreali-Occidentalia Sinica vol 24 pp 2393ndash2397 2004
[19] Z-S Zhang Y-H XiaoM Luo et al ldquoConstruction of a geneticlinkage map and QTL analysis of fiber-related traits in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 144 no 1-2 pp91ndash99 2005
[20] H-B Zhang Y Li BWang andPWChee ldquoRecent advances incotton genomicsrdquo International Journal of Plant Genomics vol2008 Article ID 742304 20 pages 2008
[21] K Arumuganathan and E D Earle ldquoNuclear DNA contentof some important plant speciesrdquo Plant Molecular BiologyReporter vol 9 no 3 pp 208ndash218 1991
[22] A H Paterson and R H Smith ldquoFuture horizons biotech-nology of cotton improvementrdquo in Cotton Origin HistoryTechnology and Production pp 415ndash432 John Wiley amp SonsNew York NY USA 1999
[23] V Tatineni R G Cantrell and D D Davis ldquoGenetic diversityin elite cotton germplasm determined by morphological char-acteristics and RAPDsrdquo Crop Science vol 36 no 1 pp 186ndash1921996
[24] C L Brubaker and J F Wendel ldquoRFLP diversity in cottonrdquo inGenetic Improvement of Cotton Emerging Technologies pp 81ndash101 Science Publishers Enfield NH USA 2001
[25] N D Young ldquoConstructing a plant genetic linkage map withDNA markersrdquo in DNA-Based Markers in Plants pp 39ndash57 Kluwer Academic Publishers Dordrecht The Netherlands1994
[26] M Agarwal N Shrivastava andH Padh ldquoAdvances inmolecu-lar marker techniques and their applications in plant sciencesrdquoPlant Cell Reports vol 27 no 4 pp 617ndash631 2008
[27] S Preetha and T S Raveendren ldquoMolecular marker technologyin cottonrdquo Biotechnology and Molecular Biology Reviews vol 3no 2 pp 32ndash45 2008
[28] J R Andersen and T Lubberstedt ldquoFunctional markers inplantsrdquo Trends in Plant Science vol 8 no 11 pp 554ndash560 2003
[29] R K Kalia M K Rai S Kalia R Singh and A K DhawanldquoMicrosatellite markers an overview of the recent progress inplantsrdquo Euphytica vol 177 no 3 pp 309ndash334 2011
[30] N Appleby D Edwards and J Batley ldquoNew technologiesfor ultra-high throughput genotyping in plantsrdquo Methods inMolecular Biology vol 513 pp 19ndash39 2009
[31] Q H Xu X L Zhang and Y C Nie ldquoGenetic diversityevaluation of cultivars (G hirsumtum L) from the Changjiangriver valley and Tellow river valley by RAPD markersrdquo ActaGenetica Sinica vol 28 no 7 pp 683ndash690 2001
[32] H J Lu and G O Myers ldquoGenetic relationships and discrim-ination of ten influential upland cotton varieties using RAPDmarkersrdquoTheoretical and Applied Genetics vol 105 no 2-3 pp325ndash331 2002
[33] I Alvarez and J F Wendel ldquoCryptic interspecific introgressionand genetic differentiation within Gossypium aridum (Mal-vaceae) and its relativesrdquo Evolution vol 60 no 3 pp 505ndash5172006
[34] S Liu RGCantrell J CMcCarty Jr and JM Stewart ldquoSimplesequence repeat-based assessment of genetic diversity in cottonrace stock accessionsrdquoCrop Science vol 40 no 5 pp 1459ndash14692000
[35] L F Zhu X L Zhang and Y C Nie ldquoAnalysis of geneticdiversity in upland cotton (Gossypium hirsutum L) cultivarsfrom China and foreign countries by RAPDs and SSRsrdquo Journalof Agricultural Biotechnology vol 11 pp 450ndash455 2003
[36] M P Reddy N Sarla and E A Siddiq ldquoInter simple sequencerepeat (ISSR) polymorphism and its application in plant breed-ingrdquo Euphytica vol 128 no 1 pp 9ndash17 2002
[37] C Schlotterer ldquoThe evolution of molecular markersmdashjust amatter of fashionrdquo Nature Reviews Genetics vol 5 no 1 pp63ndash69 2004
[38] C L Brubaker and J F Wendel ldquoReevaluating the origin ofdomesticated cotton (Gossypium hirsutum Malvaceae) usingnuclear restriction fragment length polymorphisms (RFLPs)rdquoAmerican Journal of Botany vol 81 no 10 pp 1309ndash1326 1994
[39] Z H Yu Y H Park G R Lazo and R J KohelMolecularMap-ping of the Cotton Genome Agron Abstracts ASA MadisonWis USA 1997
[40] C L Brubaker A H Paterson and J F Wendel ldquoComparativegenetic mapping of allotetraploid cotton and its diploid progen-itorsrdquo Genome vol 42 no 2 pp 184ndash203 1999
[41] M Ulloa and W R Meredith Jr ldquoGenetic linkage map andQTL analysis of agronomic and fiber traits in an intraspecificpopulationrdquo Journal of Cotton Science vol 4 no 3 pp 161ndash1702000
[42] M Ulloa W R Meredith Jr Z W Shappley and A L KahlerldquoRFLP genetic linkage maps from four F
23populations and
a joinmap of Gossypium hirsutum Lrdquo Theoretical and AppliedGenetics vol 104 no 2-3 pp 200ndash208 2002
[43] A J Reinisch J-M Dong C L Brubaker D M Stelly J FWendel and A H Paterson ldquoA detailed RFLP map of cottonGossypium hirsutum x Gossypium barbadense chromosomeorganization and evolution in a disomic polyploid genomerdquoGenetics vol 138 no 3 pp 829ndash847 1994
[44] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoD-subgenome bias of Xcm resistance genes in tetraploidGossypium (cotton) suggests that polyploid formation hascreated novel avenues for evolutionrdquo Genetics vol 149 no 4pp 1987ndash1996 1998
[45] H A Erlich PCR Technology Principles and Applications forDNA Amplification W H Freeman New York NY USA 1991
[46] J G KWilliams A R Kubelik K J Livak J A Rafalski and SV Tingey ldquoDNApolymorphisms amplified by arbitrary primers
The Scientific World Journal 11
are useful as geneticmarkersrdquoNucleic Acids Research vol 18 no22 pp 6531ndash6535 1990
[47] S Khanam A Sham J L Bennetzen and M A M Aly ldquoAnal-ysis of molecular marker-based characterization and geneticvariation in date palm (Phoenix Dactylifera L)rdquo AustralianJournal of Crop Science vol 6 no 8 pp 1236ndash1244 2012
[48] K J Chalmers R Waugh J I Sprent A J Simons and WPowell ldquoDetection of genetic variation between and withinpopulations of Gliricidia sepium and G maculata using RAPDmarkersrdquo Heredity vol 69 pp 465ndash472 1992
[49] D S Multani and B R Lyon ldquoGenetic fingerprinting ofAustralian cotton cultivars with RAPD markersrdquo Genome vol38 no 5 pp 1005ndash1008 1995
[50] M KWajahatullah and J M Stewart ldquoGenomic affinity amongGossypium subgenus Sturtia species by RAPD analysisrdquo inProceeding of the Beltwide Cotton Conference National CottonCouncil p 452 Memphis Tenn USA 1997
[51] C D Geng Z Z Gong J Q Huang and Z C ZhangldquoIdentification of difference between cotton cultivars (G hirsu-tum) using the RAPD methodrdquo Jiangsu Journal of AgriculturalSciences vol 11 no 4 pp 21ndash24 1995
[52] T H Lan C G Cook and A H Paterson ldquoIdentification of aRAPDmarker linked tomale fertility restoration gene in cotton(Gossypium hirsutum L)rdquo Journal of Agricultural Genomics vol1 pp 1ndash5 1999
[53] B Shu K Fenling Z Y Yao Z G Mei Z Q Yuan and W XGang ldquoGenetic diversity analysis of representative elite cottonvarieties in three main cotton regions in China by RAPD andits relation with agronomic characteristicsrdquo Scientia AgriculturaSinica vol 34 pp 597ndash603 2001
[54] M Ulloa R G Cantrell R G Percy E Zeiger and Z Lu ldquoQTLanalysis of stomatal conductance and relationship to lint yieldin an interspecific cottonrdquo Journal of Cotton Science vol 4 no1 pp 10ndash18 2000
[55] B Bornet and M Branchard ldquoNonanchored inter simplesequence repeat (ISSR)markers reproducible and specific toolsfor genome fingerprintingrdquo Plant Molecular Biology Reportervol 19 no 3 pp 209ndash215 2001
[56] T M Culley and A D Wolfe ldquoPopulation genetic structureof the cleistogamous plant species Viola pubescens Aiton (Vio-laceae) as indicated by allozyme and ISSR molecular markersrdquoHeredity vol 86 no 5 pp 545ndash556 2000
[57] J B Wang ldquoISSR markers and their applications in plantgeneticsrdquo Yi Chuan vol 24 no 5 pp 613ndash616 2002
[58] T Nagaoka and Y Ogihara ldquoApplicability of inter-simplesequence repeat polymorphisms inwheat for use asDNAmark-ers in comparison to RFLP and RAPDmarkersrdquoTheoretical andApplied Genetics vol 94 no 5 pp 597ndash602 1997
[59] M Z Galvan B Bornet P A Balatti and M BranchardldquoInter simple sequence repeat (ISSR) markers as a tool for theassessment of both genetic diversity and gene pool origin incommon bean (Phaseolus vulgaris L)rdquo Euphytica vol 132 no3 pp 297ndash301 2003
[60] A Shi S Kantartzi M Mmbaga and P Chen ldquoDevelopmentof ISSR PCR markers for diversity study in dogwood (Cornusspp)rdquo Agriculture and Biology Journal of North America vol 1pp 189ndash194 2010
[61] M W Blair O Panaud and S R McCouch ldquoInter-simplesequence repeat (ISSR) amplification for analysis of microsatel-litemotif frequency and fingerprinting in rice (Oryza sativa L)rdquoTheoretical and Applied Genetics vol 98 no 5 pp 780ndash7921999
[62] B Bornet C Muller F Paulus and M Branchard ldquoHighlyinformative nature of inter simple sequence repeat (ISSR)sequences amplified using tri- and tetra-nucleotide primersfrom DNA of cauliflower (Brassica oleracea var botrytis L)rdquoGenome vol 45 no 5 pp 890ndash896 2002
[63] M Sica G Gamba S Montieri L Gaudio and S AcetoldquoISSR markers show differentiation among Italian populationsofAsparagus acutifolius Lrdquo BMCGenetics vol 6 article 17 2005
[64] P Vos R Hogers M Bleeker et al ldquoAFLP a new technique forDNA fingerprintingrdquo Nucleic Acids Research vol 23 no 21 pp4407ndash4414 1995
[65] G O Myers B Jiang M W Akash A Badigannavar and SSaha ldquoChromosomal assignment of AFLP markers in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 165 no 2 pp391ndash399 2009
[66] K Lukonge L Hersalman and M T Labuschagne ldquoGeneticdiversity of tanzanian cotton revealed by AFLP analysisrdquo inProceedings of the African Crop Science Conference vol 8 pp773ndash776 2007
[67] N Murtaza ldquoCotton genetic diversity study by AFLP markersrdquoElectronic Journal of Biotechnology vol 9 no 4 pp 456ndash4602006
[68] M Zhong J CMcCarty J N Jenkins and S Saha ldquoAssessmentof day-neutral backcross populations of cotton using AFLPmarkersrdquo Journal of Cotton Science vol 6 no 2 pp 97ndash1032002
[69] A Rakshit S Rakshit J Singh et al ldquoAssociation of AFLPand SSR markers with agronomic and fibre quality traits inGossypium hirsutum Lrdquo Journal of Genetics vol 89 no 2 pp155ndash162 2010
[70] A Badigannavar and G Myers ldquoGenetic analysis of AFLPmarkers associated with seed quality traits in upland cotton(Gossypium hirsutum)rdquo in Beltwide Cotton Conferences NewOrleans La USA 2010
[71] M K Altaf J M C D Stewart M K Wajahatullah J Zhangand R G Cantrell ldquoMolecular and morphological geneticsof a trispecies F2 population of cottonrdquo in Proceedings of theBeltwide Cotton Conferences vol 1 pp 448ndash452 New OrleansLa USA January 1997
[72] M K Rana and K V Bhat ldquoA comparison of AFLP andRAPD markers for genetic diversity and cultivar identificationin cottonrdquo Journal of Plant Biochemistry and Biotechnology vol13 no 1 pp 19ndash24 2004
[73] J-M Lacape T-B Nguyen S Thibivilliers et al ldquoA combinedRFLP-SSR-AFLP map of tetraploid cotton based on a Gossyp-ium hirsutum times Gossypium barbadense backcross populationrdquoGenome vol 46 no 4 pp 612ndash626 2003
[74] D TautzM Trick andG A Dover ldquoCryptic simplicity in DNAis amajor source of genetic variationrdquoNature vol 322 no 6080pp 652ndash656 1986
[75] S Saha J Wu J N Jenkins et al ldquoBreeding and genetics effectof chromosome substitutions from Gossypium barbadense L 3-79 into G hirsutum L TM-1 on agronomic and fiber traitsrdquoJournal of Cotton Science vol 8 no 3 pp 162ndash169 2004
[76] O U K Reddy A E Pepper I Abdurakhmonov et al ldquoNewdinucleotide and trinucleotide microsatellite marker resourcesfor cotton genome researchrdquo Journal of Cotton Science vol 5no 2 pp 103ndash113 2001
[77] T B Nguyen M Giband P Brottier A M Risterucci and JM Lascape ldquoWide coverage of the tetraploid cotton genomeusing newly developed microsatellite markersrdquoTheoretical andApplied Genetics vol 109 no 1 pp 167ndash175 2004
12 The Scientific World Journal
[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
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BioinformaticsAdvances in
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Evolutionary BiologyInternational Journal of
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ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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International Journal of
Microbiology
The Scientific World Journal 5
Table2Anoverview
ofgenetic
diversity
studies
incotto
nusingmolecular
markers
Marker
Cou
ntry
Popu
latio
ntype
Size
References
RAPD
s
USA
16near-hom
ozygou
selitec
ottongeno
types
80RA
PDprim
ers
[23]
Pakista
n31
Gossypium
species3subspecies
and1interspecifich
ybrid
45RA
PDprim
ers
[115]
USA
10varie
tieso
fUplandcotto
n86
RAPD
prim
ers
[32]
Pakista
n30
cultivarsof
Garboretum
50RA
PDprim
ers
[169]
Iran
13F 1
andF 2
cotto
ngeno
types(Gossypium
hirsutum
)obtainedby
crossin
g30
RAPD
prim
ers
[170]
India
Intraspecific
cotto
nF 1
hybrid
andits
parents
20RA
PDprim
ers
[171]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
40RA
PDprim
ers
[172]
SSRs
USA
24cultivarsof
Ghirsutum
88SSRprim
ers
[173]
China
39accessions
ofG
arboreum
358SSRprim
ers
[174]
China
108accessions
ofAs
iatic
cotto
nand1G
herbaceum
60SSRprim
ers
[175]
China
43sourceso
fUplandcotto
ngerm
plasm
36SSRprim
ers
[124]
France
47geno
typeso
ftetraploidcotto
n320SSRprim
ers
[176]
USA
96accessions
ofG
arboreum
115Genom
icandES
T-SSRs
[177]
Pakistan
8accessions
ofG
hirsutum
32SSRprim
ers
[178]
China
59geno
typeso
fGhirsutum
40ES
T-SSRprim
ers
[179]
Greece
29geno
typeso
fGhirsutum
andan
interspecific
hybrid
12SSRprim
erpairs
[180]
China
56accessions
ofSeaisla
ndcotto
n237SSRprim
ers
[125]
Egypt
28geno
typeso
fEgyptiancotto
n6SSRand5ES
T-SSRprim
er[2]
Pakista
n19
geno
typeso
fBtcotton
104SSRprim
ers
[107]
USA
193cultivarsof
Uplandcotto
n44
8SSRprim
ers
[126]
USA
378accessions
ofG
hirsutum
and3of
Gbarbadense
120SSRprim
ers
[181]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
4SSRprim
ers
[172]
AFL
Ps
USA
11accessions
ofG
hirsutum
and2fro
meach
ofG
arboreum
Gherbaceum
andG
barbadense
4EcoR
I-MseIp
rimersfor
AFL
P[106]
Belgium
Uplandcotto
nwild
species(G
raim
ondiiand
Gthurbrii)
andtheirB
C 3progenies
5AFL
Pprim
ers
[117]
USA
3diploidspecieso
fGossypium
3G
barbadensecultivarsand43
Ghirsutum
accessions
20AFL
Pprim
ers
[13]
USA
29accessions
from
fives
pecies
oftheg
enus
Gossypium
16AFL
Pprim
ers
[17]
India
24lin
esof
Ghirsutum
L6AFL
Pprim
ers
[182]
Norway
131a
ccessio
nsof
Gbarbadan
se8AFL
Pprim
ers
[183]
ISSR
s
Iran
13F 1
andF 2
cotto
ngeno
types(Gossypium
hirsutum
)8ISSR
prim
ers
[170]
Egypt
28Eg
yptia
ncotto
ngeno
types
5ISSR
prim
ers
[2]
India
Intraspecific
cotto
nF 1
hybrid
andits
parents
19ISSR
prim
ers
[171]
Iran
11geno
typeso
fGhirsutum
inclu
ding
6F 2
progenies
20ISSR
prim
ers
[172]
SNPs
Pakista
n2cultivarsof
tetraploid
cotto
nPrim
ersc
orrespon
dto
FIF1
gene
[184]
USA
24lin
esof
cotto
n270SN
Plociand92
Indel
[99]
6 The Scientific World Journal
genetic diversity using RAPD markers during 90s Geneticdiversity of 16 elite homozygous genotypes obtained fromthe inter-specific hybridization was studied using 80 RAPDmarkers [23] RAPD markers were used to differentiate theG hirsutum lines from the G arboretum [113] Similarly25 short duration genotypes of cotton were analyzed usingarbitrary primers [114] Later [115] studied genetic diversityof 31 Gossypium species 3 subspecies and 1 interspecifichybrid using 45 RAPD primers and the results showed thatgenetic relationship of many species is related to the centerof origin Recently genetic diversity in 18 cotton genotypes ofPakistan studied by 5 RAPD primers showed that two diversegenotypes of cotton (CIM-240 and CIM-443) have resistanceagainst cotton leaf curl virus [116]
AFLP technique was also used to distinguish the dif-ferences among diploid and tetraploid species of cotton byutilizing the variations in ribosomal RNA genes [106] Thegenetic diversity between the upland cotton wild species (Graimondii G thurberii and G sturtianum) and their BC
3
progenies was evaluated usingAFLPmarkers [117] Intra- andinterspecific relatedness of theG barbadense G arboreumGraimondii and G hirsutum are determined by AFLPs whichdemonstrated its usefulness for genetic relatedness acrosswide range of species [17] The relationship between the par-ents and four day neutral backcross generations of cotton wasdetermined using 43 AFLP markers [68] Comparative studywas conducted to evaluate AFLP and RAPD techniques using16 diploid cotton genotypes and it was concluded that AFLPmarkers are more efficient for polymorphism detection andfor analyzing of genetic diversity as compared to RAPDs [72]Similarly genetic diversity of 26 Tanzanian cotton genotypes(Gossypiumhirsutum L) was studied using theAFLPmarkers[66] The results of this study indicated the high values ofgenetic similarity which show the lower genetic diversityamong Tanzanian cotton cultivars Reference [65] mapped98 AFLP markers and assigned 22 distinctive chromoso-mal positions using cytogenetic deletion stocks Mappinginformation enhanced the utilization of AFLPs and can beused to saturate the existing marker frequency over differentchromosomes
In cotton SSRs are considered as a new class of DNAmarkers which hastened cotton genetic diversity and map-ping studies [27] and are important source to observe thetranscribed genes [118] There are multiple reports aboutusing the SSR markers for genetic diversity Reference [119]identified 71 SSR loci with 65 primer pairs and placed themondistinctive chromosomes of cotton Genetic diversity amongUS and Australian cultivars and day neutral lines of Ghirsutum was also analyzed by SSR markers [120]
Further saturation of SSR markers was extended by addi-tion of 204 markers which exhibited 261 segregating bandsgiving rise to 233 mapped loci in cotton [77] Interspecificpolymorphism between G barbadense and G hirsutum wasalso studied using SSR markers and results showed thatpolymorphism between species was high but it was lowwithin species [121] Reference [122] developed new SSRmarkers analyzed the status of 23 chromosomes and foundthat the inter loci distance was 49 cM Diversity among52 different G hirsutum cultivars was studied by 31 SSR
primer pairs and successfully discriminated the 52 cultivarsthrough broader allelic coverage [123] Similarly geneticdiversity of 43 upland cotton varieties [124] 56 sea-islandcotton accessions [125] 19 Bt cotton genotypes [107] 50representative Pakistani genotypes [104] and 193 uplandcotton cultivars [126] were evaluated using 36 237 104 70and 448 SSR markers respectively SSRs have also been usedto assess the genetic purity of the cotton hybrids [127] anddemonstrated as an effective tool for hybrid identification
Recent developments in next generation sequencing(NGS) and RNA-seq technology have generated high-throughput sequence data which facilitated the identificationof SNPs as effective and highly saturated markers for geneticstudies in cotton Genetic variations within and betweenthe different species of cotton have been characterized by1000 SNPs and 279 In-Dels from the 270 and 92 locisegregating in G barbadense and G hirsutum to providemapped molecular markers for crosses within species andintrogression of foreign germplasm in cotton [99] A genomereduction experiment based on the restriction site conserva-tion (GR-RSC) and previously generated assembly of expresssequence tags (ESTs) were used to discover the SNPs in 4accessions of G hirsutum and G barbadense A total 11834and 1679 non-genic and 4327 genic SNPs were identified inthe GR-RSC and EST assemblies using highly conservationparameters The KASPer assays were used to target the 1052(704 nongenic and 348 genic) genome specific SNPs betweenthe G hirsutum accessions [93] The assay then tested forthe Mendelian segregation ratio in the F
2population derived
from a cross of upland cotton (G hirsutum) cultivars
32 QTLs Mapping for Important Economic Traits in Cot-ton The regions in genomes to have genes linked with aquantitative trait are known as quantitative trait loci QTLs[128] and the process of developing linkage maps andperforming QTL analysis is referred to as QTLmapping [129130] QTL analysis stands on the principal of identifying aconnection among phenotype and genotype ofmarkers [128]The QTLs identified in cotton germplasm using differentmarker technologies are summarized in Table 3
RFLPs have been widely used to map genes of economicinterest in cotton Previously RFLP map of G hirsutum andG barbadensewas used tomap 14QTLs for fiber related traits[131] Similarly genes influencing density of stem and leaftrichomes [132] high gossypol plant and low seed gossypolcontents [117] were confined by RFLP markers Reference[131] developed an RFLP map of 261 markers distributedamong 26 linkage groups using F
2plants from an interspecific
cross Another genetic linkage map was developed usingRFLP markers and 26 QTLs were recognized for agronomicand fiber quality traits [41] Later on RFLP based QTLmapping was extended to leaf chlorophyll contents [133]Backcross population of G hirsutum and G barbadense wasused to map 28 9 and 8 QTLs for fiber length lengthuniformity and short fiber contents respectively using the262 RFLP markers [134]
RAPDs have also been widely used for QTL mappingin cotton however lack of reproducibility and unknown
The Scientific World Journal 7
Table3Anoverview
ofQTL
studies
incotto
n
Traits
Descriptor
Popu
latio
nSize
Marker(nu
mbera
ndtype)
QTL
snum
ber
Reference
Fiberq
uality
FSFLandFF
F 2171
RFLP
sand
85RA
PDs
13[135]
FSF 2
186
217SSRs800
RAPD
sUBC
and1040
OPE
RON
2[153]
LYLPSW
NSUQSFFL
FE
FTFFandIF
F 2120
144AFL
PsR
FLPs
and150SSRs
28[14
1]FS
FE
FLFU
LPandFF
F 2117
290SSRs
and9AFL
Ps16
[19]
FFBC
3F2
3662
262RF
LPs
41[185]
FLFLU
andSFC
BC3F
23662
262RF
LPs
45[134]
FSFE
FUFLandFF
RILrsquos
270
7508
SSRs384
SRAPs
and740IT-ISJs
13[186]
FLFSFF
andFE
F 2mdash
1378
SSRs
39[136]
FSFLFFFMTFE
andSFI
RILrsquos
180
4106
SSRsA
FLPsR
APD
sand
SRAPs
48[187]
FEFLFS
FFandFU
CP172
16052SSRs
63[188]
Fibera
ndagrono
mical
SCYLYLPBW
SIFM
TPE
RWFWTFFFLFE
andFS
RILrsquos
188
141S
SRs
56[189]
Yield
andfib
er
FSFLFFFE
LPSINB
SCYandLY
RILrsquos
258
2131
SSRs
53[19
0]
NB
BWSILPLISC
YLYFLFS
FFFE
andFU
4WCandinbred
lines
280
6123
SSRs
andES
T-SSRs
31[138]
SCYLYN
BBW
LPSILIand
FBN
RILrsquos
andIF2
180
2675
EST-SSRs
111
[191]
PHFBN
BWLPLISILYFLFS
FE
FFandFU
Ghirsutum
accessions
81121S
SRs
180
[3]
LISILYSCY
NSB
andFS
F 269
834SSRs437
SRAPs107
RAPD
sand
16RE
MAPs
52[192]
Morph
ological
LBNOSL1L1W1L2
W2L3
andW3
F 2180
261R
FLPs
62[19
3]EM
F 2andF 3
mdash40
83SSRs
54[14
0]NFB
F 2251
1165SSRs
5[19
4]Plant
architectural
PHFBL
FBN
FBA
FBL
PHandNMUB
RILrsquos
180
2130
SSRs2
RAPD
sand
1SRA
P16
[137]
NB
numbero
fbollsperp
lantB
Wb
ollw
eightSIseedindexLP
lintp
ercentL
Ilin
tind
exSIseed
indexSC
Yseed
cotto
nyieldperp
lantLY
linty
ield
perp
lantF
Lfib
erleng
thF
Sfib
erstr
ength
FEfi
ber
elong
ation
FUfiberu
niform
ityratio
FY
fiber
yello
wnessFFfib
erfin
enessFM
Tfib
ermaturityP
Hplant
heightFBL
fruitbranch
leng
thFBN
fruitbranch
numberFB
Afruitbranch
angleFL
Ufiberlength
unifo
rmitySFC
sho
rtfib
ercontentFR
fiberreflectanceSW
seedweightNSnu
mbero
fseeds
perp
lantU
Qupp
erqu
artilelengthSFsho
rtfib
ercontentFT
fibertenacityIFim
maturefi
bercon
tentSFIsho
rtfib
erindexNSB
num
bero
fseeds
perb
ollEM
earlymaturityN
MUB
lowerm
iddleandup
sideb
olln
umberNFB
nod
etofirstfruitin
gbranchLBN
Olob
enum
bersSL1sub
lobe
numbero
nthem
ainlobeL1
main-lobe
leng
thW
1main-lobe
widthL2second
-lobe
leng
thW
2second
-lobe
widthL3third
-lobe
leng
thW
3third
-lobe
leng
thPER
perim
eterW
Fweightfi
tnessWT
wallthicknessFBL
PHratioof
fruit
branch
leng
thto
planth
eightRILrsquosrecom
binant
inbred
linesIF2immortalized
F2s4W
Cfour
way
crossCP
com
positec
rossand
BC3F
2=backcrossfam
ilies
8 The Scientific World Journal
chromosomal positions remained main disadvantages whichrestricted the use of RAPDs in advanced studies Refer-ence [135] used 85 RAPD markers and identified 13 QTLsassociated to the fiber quality in the F
2population derived
from the G hirsutum and G barbadense cross There arenumerous studies on using the RAPDs for QTL mappingalong with other molecular markers (Table 3) An extensiveSSR genotyping was conducted over F
2populations from 3
diverse upland cotton genotypes using 1378 markers and 39fiber related QTLs were identified [136] Recombinant inbredlines (RILs) are also important mapping populations andseveral QTLs related to plant architecture [137] yield [3] andfiber quality [19] have been identified in upland cotton usingRILs About 31QTLs linked to the yield and fiber quality traitsare detected bywide array of SSR and EST SSRmarkers (6123)in 4 way cross populations developed from the 4 inbred linesof G hirsutum [138] A genetic linkage map of the tetraploidcotton was developed using 1601 pairs of SSR and 247 SNPmarkers [139] The genetic map consisted of the 2072 locicovering 3380 cm of the cotton genome Two F
2populations
were generated by the crosses of upland cotton cultivars and4083 SSR markers were used for QTL analysis which detect54 QTLs linked to early maturity [140]
A total of 144 primer combinations of AFLPs and 150 ofSSRs were used to detect 28 QTLs related to the fiber traits[141] To know the significant threshold for the LR statisticspermutation tests were carried out afterwhich 7QTLs remainsignificant RIL lines developed from the intraspecific cross ofupland cotton are used to detect the 12 epistatic and 4 mainQTLs related to the plant architectural traits by 2130 SSR 2RAPD and 1 SRAP markers [137]
Conclusively huge arrays of QTLs have been identifiedusing multiple molecular marker technologies Descriptionof stable QTL from diverse generations common QTL fromvarious populations and homologous QTLs raises the infor-mation on the genetic base Information about distributionof important QTLs in the genome of cotton is very importantand promises the future strategy for marker assisted breed-ing Cotton Gen serves as an important database for suchinformation and currently this database has 988 QTLs for25 different traits (httpwwwcottongenorgdataqtl) whichcan be surveyed according to objectivity
33 Genome Wide Association Studies (GWAS) in CottonAssociation mapping also known as linkage disequilibrium(LD) mapping has appeared as a tool to determine thevariation in complex traits using historical and evolutionaryrecombination actions at the population level [142] In asso-ciation mapping nonstructured populations are phenotypedand genotyped to identify the trait associated with marker[143] This results into capture of wider recombination andhigher resolution mapping as compared to linkage mapping[144] The applications of association mapping for cottonassist extensive employment of natural genetic diversity con-served within the worldwide collections of cotton germplasm[145] as in other plant germplasm resources Turning theefforts of gene-tagging from biparental QTL mapping to LD-based association study promise the productive employment
of ex situ conserved genetic diversity of global germplasmresources of cotton [10] The cotton genome may need fewnumbers of markers for productive associating mappingof complex traits which is also reported for other crops[146] Regarding the tetraploid genome of cotton with atotal recombination length of about 5200 cm and an average400 kb per cm [22] the LD block sizes of sim5-6 cm distanceis sufficient to conduct an association mapping of differenttraits that would require a maximum of sim1000 polymorphicmarkers for successful and reliable associationmapping [147]Extent of genome-wide LD and association mapping offiber quality traits were reported using 95 SSR markers in285 exotic accessions of G hirsutum comprised of 208 lan-draces and 77 varieties [10] Similarly LD-based associationmapping was conducted for fiber quality traits in 335 Ghirsutum germplasm using 202 SSR markers [147] Progressin genome sequencing technology provides an opportunity toproduce large size genotypic data which supports associationmapping over QTL mapping and because of this associationmapping is becoming more common [148]
34 Marker Assisted Selection (MAS) in Cotton Markerassisted selection (MAS) is a procedure by which a phenotypeis selected on the basis of genotype of a marker [128]Selecting the plants in the segregating population that havethe suitable genes combinations is the important componentof plant breeding [149] Once the markers tightly linked tothe genes have been detected breeders may use particularDNA marker to identify the plants carry the genes [150]The effectiveness and cost of MAS are influenced by themarker technique therefore it must be selected carefully[151] During the past two decades RAPDs techniqueshave been used for MAS for getting the glanded plantsand glandless seeds in the interspecific population of Gsturtianum and other species [152] It was exposed that DNAmarkers connected to the major QTL (QTLFS1) for fiberstrength could be utilized inMAS to increase fiber strength ofcommercial varieties in segregating populations [153] SomeRAPD markers were developed into locus specific sequencecharacterized amplified region (SCAR) markers to screen theBC1F4upland cotton For example SCAR 1920marker for the
major fiber strength QTL was developed and has been usedfor selecting desirable genotypes [154] Screening of the SNPswhich aremapped on chromosome 10 recognized extra 3 SNPmarkers thatwere associatedwith blue disease resistance gene(Cbd) which were employed to efficiently characterize a traitallowing MAS for strong levels of blue disease resistance incotton breeding programs [155]
4 Cotton Draft Genome and Its Implication
The increasing information of DNA sequencing allows thediscovery of genes and molecular markers associated withdifferent traits opening new avenues for crop improvement[148] Sequencing of DNA promises to display the spectrumof diversity in the genus Gossypium The tetraploid cottonspecies (2119899 = 4119909 = 52) such as G hirsutum and G bar-
The Scientific World Journal 9
badense are thought to have developed by an allopoly-ploidization that happened nearly 1-2 million years ago inwhich a D-genome species is pollen parent and species of anA-genome is maternal parent [12 156] It is essential to havea basic awareness of the structure of the component genomesto understand the cultivated polyploid genomes their evo-lution and interaction between their subgenomes Towardthe long-term aim of characterizing the diversity amongcotton genomes the cotton geneticists have prioritized the Dgenome progenitor G raimondii for complete sequencing Graimondii has a sim880Mb genome [157] the smallest genomein the genus Gossypium at sim60 of the size of diploid A-genome and 40 of the tetraploids [158] A physical map ofG raimondii genome was assembled and several evidencesreferred that the G raimondii genome is composed of twodifferent qualitative components one that is gene-rich andanother that is repeat-rich [158] About 40976 protein codinggenes and 2355 syntenic blocks identified in the genome ofG raimondii [159] Similarly the sequencing and assemblingof G arboreum genome depicted that 685 of the genomeis covered by repetitive DNA sequences and about 41330protein-coding genes were predicted in the genome of Garboreum [160]
5 Future Prospects
Cotton is a major source of foreign exchange for manycountries around the globe therefore major focus remainsthe enhancement of yield and quality of fiber This challengecan be accomplished by introducing new alleles from wildspecies [161 162] and use of modern molecular technologieshelping in increasing genetic gain of economic traits In thisscenario it is believed that sequencing of the G raimondii[159] and G arboreum [160] draft genomes will facilitate thegene discovery of important traits These genome resourcescan also be used for discovery of high-throughput markerplatforms like Select SNP arrays These high-throughputDNAmarkers will be helpful in recognizing the cotton geno-types carrying desired characters and was successfully usednot only to study the genetic diversity but to develop linkagemaps and mapping agronomic traits [12 20] which arenecessary for acceleration of varietal development Althoughthe QTL mapping for the various traits that is fiber yieldand quality [131] drought tolerance [133] disease resistance[163 164] and pests resistance [165] have been accomplishedin cotton but these may not be helpful to clone causal genesdue to lower marker densities In general the choice of amolecular marker technique is based on reliability statisticalpower and level of polymorphisms Since their inventionthey are being continuously modified for improved utilityto solve many problems and to bring forth automationWhen these markers techniques reach a greater degree ofautomation then it will be suitable to use DNA markersdirecting to a new ldquoGreen Revolutionrdquo in the agriculturalworld
Presently the enormous development of more efficientDNAmarkers will go on in the future because they can serveas an important tool for the plant breeders and geneticists
to develop the cultivars of cotton that are demanded bythe society It has been proposed that SNPs marker willhave large influence on MAS and mapping studies in futuredue to high abundance and development of sophisticateddetection system [195] GBS will clearly become the markergenotyping platform in coming years So the development ofnovel markers such as GBS and SNPs and the accessibility ofmodern technologies such as DNA Chips and microarrayshasten genome mapping and subsequent gene discovery inthe cotton for efficient cotton varietal development
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgment
We are highly thankful to Dr Awais Rasheed (CIMMYTChina) for his valued inputs and comments
References
[1] USDA Cotton and Wool Year book Dataset 2011 httpusdamannlibcornelleduMannUsdaviewDocumentInfododocu-mentID=128
[2] K F Abdellatif Y A Khidr Y M Mansy M M Lawendey andY A Soliman ldquoMolecular diversity of Egyptian cotton (Gossyp-ium barbadense L) and its relation to varietal developmentrdquoJournal of Crop Science and Biotechnology vol 15 pp 93ndash992012
[3] T Zhang N Qian X Zhu et al ldquoVariations and transmissionof QTL alleles for yield and fiber qualities in upland cottoncultivars developed in Chinardquo PLoS ONE vol 8 no 2 ArticleID e57220 2013
[4] H J Kim and B A Triplett ldquoCotton fiber growth in plantaand in vitro Models for plant cell elongation and cell wallbiogenesisrdquo Plant Physiology vol 127 no 4 pp 1361ndash1366 2001
[5] Y-L Ruan D J Llewellyn and R T Furbank ldquoSuppressionof sucrose synthase gene expression represses cotton fiber cellinitiation elongation and seed developmentrdquo Plant Cell vol 15no 4 pp 952ndash964 2003
[6] Y-M Qin and Y-X Zhu ldquoHow cotton fibers elongate a tale oflinear cell-growth moderdquo Current Opinion in Plant Biology vol14 no 1 pp 106ndash111 2011
[7] P A Fryxell ldquoA revised taxonomic interpretation of GossypiumL (Malvaceae )rdquo Rheedea vol 2 pp 108ndash165 1992
[8] J O Beasley ldquoThe production of polyploids in gossypiumrdquoJournal of Heredity vol 31 no 1 pp 39ndash48 1940
[9] J E Endrizzi E L Turcotte and R J Kohel ldquoGenetics cytologyand evolution of Gossypiumrdquo Advances in Genetics vol 23 pp271ndash375 1985
[10] I Y Abdurakhmonov R J Kohel J Z Yu et al ldquoMoleculardiversity and associationmapping of fiber quality traits in exoticG hirsutum L germplasmrdquo Genomics vol 92 no 6 pp 478ndash487 2008
[11] J F Wendel and R C Cronn ldquoPolyploidy and the evolutionaryhistory of cottonrdquo Advances in Agronomy vol 78 pp 139ndash1862003
10 The Scientific World Journal
[12] Z J Chen B E Scheffler E Dennis et al ldquoToward sequencingcotton (Gossypium) genomesrdquo Plant Physiology vol 145 no 4pp 1303ndash1310 2007
[13] M J Iqbal O U K Reddy K M El-Zik and A E PepperldquoA genetic bottleneck in the lsquoevolution under domesticationrsquoof upland cotton Gossypium hirsutum L examined using DNAfingerprintingrdquoTheoretical and Applied Genetics vol 103 no 4pp 547ndash554 2001
[14] J O Beasley ldquoThe origin of American tetraploid GossypiumspeciesrdquoThe American Naturalist vol 74 pp 285ndash286 1940
[15] J O Beasley ldquoMeiotic chromosome behavior in species specieshybrids haploids and induced polyploids ofGossypiumrdquoGenet-ics vol 27 no 1 pp 25ndash54 1942
[16] J F Wendel C L Brubaker and A E Percival ldquoGeneticdiversity in Gossypium hirsutum and the origin of uplandcottonrdquoAmerican Journal of Botany vol 79 no 11 pp 1291ndash13101992
[17] A M Abdalla O U K Reddy K M El-Zik and A E PepperldquoGenetic diversity and relationships of diploid and tetraploidcottons revealed using AFLPrdquoTheoretical and Applied Geneticsvol 102 no 2-3 pp 222ndash229 2001
[18] X L Song X Z Sun T Z Zhang and H G Wang ldquoAdvanceson genetic diversity of cotton (Gossypium)rdquo Acta BotanicaBoreali-Occidentalia Sinica vol 24 pp 2393ndash2397 2004
[19] Z-S Zhang Y-H XiaoM Luo et al ldquoConstruction of a geneticlinkage map and QTL analysis of fiber-related traits in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 144 no 1-2 pp91ndash99 2005
[20] H-B Zhang Y Li BWang andPWChee ldquoRecent advances incotton genomicsrdquo International Journal of Plant Genomics vol2008 Article ID 742304 20 pages 2008
[21] K Arumuganathan and E D Earle ldquoNuclear DNA contentof some important plant speciesrdquo Plant Molecular BiologyReporter vol 9 no 3 pp 208ndash218 1991
[22] A H Paterson and R H Smith ldquoFuture horizons biotech-nology of cotton improvementrdquo in Cotton Origin HistoryTechnology and Production pp 415ndash432 John Wiley amp SonsNew York NY USA 1999
[23] V Tatineni R G Cantrell and D D Davis ldquoGenetic diversityin elite cotton germplasm determined by morphological char-acteristics and RAPDsrdquo Crop Science vol 36 no 1 pp 186ndash1921996
[24] C L Brubaker and J F Wendel ldquoRFLP diversity in cottonrdquo inGenetic Improvement of Cotton Emerging Technologies pp 81ndash101 Science Publishers Enfield NH USA 2001
[25] N D Young ldquoConstructing a plant genetic linkage map withDNA markersrdquo in DNA-Based Markers in Plants pp 39ndash57 Kluwer Academic Publishers Dordrecht The Netherlands1994
[26] M Agarwal N Shrivastava andH Padh ldquoAdvances inmolecu-lar marker techniques and their applications in plant sciencesrdquoPlant Cell Reports vol 27 no 4 pp 617ndash631 2008
[27] S Preetha and T S Raveendren ldquoMolecular marker technologyin cottonrdquo Biotechnology and Molecular Biology Reviews vol 3no 2 pp 32ndash45 2008
[28] J R Andersen and T Lubberstedt ldquoFunctional markers inplantsrdquo Trends in Plant Science vol 8 no 11 pp 554ndash560 2003
[29] R K Kalia M K Rai S Kalia R Singh and A K DhawanldquoMicrosatellite markers an overview of the recent progress inplantsrdquo Euphytica vol 177 no 3 pp 309ndash334 2011
[30] N Appleby D Edwards and J Batley ldquoNew technologiesfor ultra-high throughput genotyping in plantsrdquo Methods inMolecular Biology vol 513 pp 19ndash39 2009
[31] Q H Xu X L Zhang and Y C Nie ldquoGenetic diversityevaluation of cultivars (G hirsumtum L) from the Changjiangriver valley and Tellow river valley by RAPD markersrdquo ActaGenetica Sinica vol 28 no 7 pp 683ndash690 2001
[32] H J Lu and G O Myers ldquoGenetic relationships and discrim-ination of ten influential upland cotton varieties using RAPDmarkersrdquoTheoretical and Applied Genetics vol 105 no 2-3 pp325ndash331 2002
[33] I Alvarez and J F Wendel ldquoCryptic interspecific introgressionand genetic differentiation within Gossypium aridum (Mal-vaceae) and its relativesrdquo Evolution vol 60 no 3 pp 505ndash5172006
[34] S Liu RGCantrell J CMcCarty Jr and JM Stewart ldquoSimplesequence repeat-based assessment of genetic diversity in cottonrace stock accessionsrdquoCrop Science vol 40 no 5 pp 1459ndash14692000
[35] L F Zhu X L Zhang and Y C Nie ldquoAnalysis of geneticdiversity in upland cotton (Gossypium hirsutum L) cultivarsfrom China and foreign countries by RAPDs and SSRsrdquo Journalof Agricultural Biotechnology vol 11 pp 450ndash455 2003
[36] M P Reddy N Sarla and E A Siddiq ldquoInter simple sequencerepeat (ISSR) polymorphism and its application in plant breed-ingrdquo Euphytica vol 128 no 1 pp 9ndash17 2002
[37] C Schlotterer ldquoThe evolution of molecular markersmdashjust amatter of fashionrdquo Nature Reviews Genetics vol 5 no 1 pp63ndash69 2004
[38] C L Brubaker and J F Wendel ldquoReevaluating the origin ofdomesticated cotton (Gossypium hirsutum Malvaceae) usingnuclear restriction fragment length polymorphisms (RFLPs)rdquoAmerican Journal of Botany vol 81 no 10 pp 1309ndash1326 1994
[39] Z H Yu Y H Park G R Lazo and R J KohelMolecularMap-ping of the Cotton Genome Agron Abstracts ASA MadisonWis USA 1997
[40] C L Brubaker A H Paterson and J F Wendel ldquoComparativegenetic mapping of allotetraploid cotton and its diploid progen-itorsrdquo Genome vol 42 no 2 pp 184ndash203 1999
[41] M Ulloa and W R Meredith Jr ldquoGenetic linkage map andQTL analysis of agronomic and fiber traits in an intraspecificpopulationrdquo Journal of Cotton Science vol 4 no 3 pp 161ndash1702000
[42] M Ulloa W R Meredith Jr Z W Shappley and A L KahlerldquoRFLP genetic linkage maps from four F
23populations and
a joinmap of Gossypium hirsutum Lrdquo Theoretical and AppliedGenetics vol 104 no 2-3 pp 200ndash208 2002
[43] A J Reinisch J-M Dong C L Brubaker D M Stelly J FWendel and A H Paterson ldquoA detailed RFLP map of cottonGossypium hirsutum x Gossypium barbadense chromosomeorganization and evolution in a disomic polyploid genomerdquoGenetics vol 138 no 3 pp 829ndash847 1994
[44] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoD-subgenome bias of Xcm resistance genes in tetraploidGossypium (cotton) suggests that polyploid formation hascreated novel avenues for evolutionrdquo Genetics vol 149 no 4pp 1987ndash1996 1998
[45] H A Erlich PCR Technology Principles and Applications forDNA Amplification W H Freeman New York NY USA 1991
[46] J G KWilliams A R Kubelik K J Livak J A Rafalski and SV Tingey ldquoDNApolymorphisms amplified by arbitrary primers
The Scientific World Journal 11
are useful as geneticmarkersrdquoNucleic Acids Research vol 18 no22 pp 6531ndash6535 1990
[47] S Khanam A Sham J L Bennetzen and M A M Aly ldquoAnal-ysis of molecular marker-based characterization and geneticvariation in date palm (Phoenix Dactylifera L)rdquo AustralianJournal of Crop Science vol 6 no 8 pp 1236ndash1244 2012
[48] K J Chalmers R Waugh J I Sprent A J Simons and WPowell ldquoDetection of genetic variation between and withinpopulations of Gliricidia sepium and G maculata using RAPDmarkersrdquo Heredity vol 69 pp 465ndash472 1992
[49] D S Multani and B R Lyon ldquoGenetic fingerprinting ofAustralian cotton cultivars with RAPD markersrdquo Genome vol38 no 5 pp 1005ndash1008 1995
[50] M KWajahatullah and J M Stewart ldquoGenomic affinity amongGossypium subgenus Sturtia species by RAPD analysisrdquo inProceeding of the Beltwide Cotton Conference National CottonCouncil p 452 Memphis Tenn USA 1997
[51] C D Geng Z Z Gong J Q Huang and Z C ZhangldquoIdentification of difference between cotton cultivars (G hirsu-tum) using the RAPD methodrdquo Jiangsu Journal of AgriculturalSciences vol 11 no 4 pp 21ndash24 1995
[52] T H Lan C G Cook and A H Paterson ldquoIdentification of aRAPDmarker linked tomale fertility restoration gene in cotton(Gossypium hirsutum L)rdquo Journal of Agricultural Genomics vol1 pp 1ndash5 1999
[53] B Shu K Fenling Z Y Yao Z G Mei Z Q Yuan and W XGang ldquoGenetic diversity analysis of representative elite cottonvarieties in three main cotton regions in China by RAPD andits relation with agronomic characteristicsrdquo Scientia AgriculturaSinica vol 34 pp 597ndash603 2001
[54] M Ulloa R G Cantrell R G Percy E Zeiger and Z Lu ldquoQTLanalysis of stomatal conductance and relationship to lint yieldin an interspecific cottonrdquo Journal of Cotton Science vol 4 no1 pp 10ndash18 2000
[55] B Bornet and M Branchard ldquoNonanchored inter simplesequence repeat (ISSR)markers reproducible and specific toolsfor genome fingerprintingrdquo Plant Molecular Biology Reportervol 19 no 3 pp 209ndash215 2001
[56] T M Culley and A D Wolfe ldquoPopulation genetic structureof the cleistogamous plant species Viola pubescens Aiton (Vio-laceae) as indicated by allozyme and ISSR molecular markersrdquoHeredity vol 86 no 5 pp 545ndash556 2000
[57] J B Wang ldquoISSR markers and their applications in plantgeneticsrdquo Yi Chuan vol 24 no 5 pp 613ndash616 2002
[58] T Nagaoka and Y Ogihara ldquoApplicability of inter-simplesequence repeat polymorphisms inwheat for use asDNAmark-ers in comparison to RFLP and RAPDmarkersrdquoTheoretical andApplied Genetics vol 94 no 5 pp 597ndash602 1997
[59] M Z Galvan B Bornet P A Balatti and M BranchardldquoInter simple sequence repeat (ISSR) markers as a tool for theassessment of both genetic diversity and gene pool origin incommon bean (Phaseolus vulgaris L)rdquo Euphytica vol 132 no3 pp 297ndash301 2003
[60] A Shi S Kantartzi M Mmbaga and P Chen ldquoDevelopmentof ISSR PCR markers for diversity study in dogwood (Cornusspp)rdquo Agriculture and Biology Journal of North America vol 1pp 189ndash194 2010
[61] M W Blair O Panaud and S R McCouch ldquoInter-simplesequence repeat (ISSR) amplification for analysis of microsatel-litemotif frequency and fingerprinting in rice (Oryza sativa L)rdquoTheoretical and Applied Genetics vol 98 no 5 pp 780ndash7921999
[62] B Bornet C Muller F Paulus and M Branchard ldquoHighlyinformative nature of inter simple sequence repeat (ISSR)sequences amplified using tri- and tetra-nucleotide primersfrom DNA of cauliflower (Brassica oleracea var botrytis L)rdquoGenome vol 45 no 5 pp 890ndash896 2002
[63] M Sica G Gamba S Montieri L Gaudio and S AcetoldquoISSR markers show differentiation among Italian populationsofAsparagus acutifolius Lrdquo BMCGenetics vol 6 article 17 2005
[64] P Vos R Hogers M Bleeker et al ldquoAFLP a new technique forDNA fingerprintingrdquo Nucleic Acids Research vol 23 no 21 pp4407ndash4414 1995
[65] G O Myers B Jiang M W Akash A Badigannavar and SSaha ldquoChromosomal assignment of AFLP markers in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 165 no 2 pp391ndash399 2009
[66] K Lukonge L Hersalman and M T Labuschagne ldquoGeneticdiversity of tanzanian cotton revealed by AFLP analysisrdquo inProceedings of the African Crop Science Conference vol 8 pp773ndash776 2007
[67] N Murtaza ldquoCotton genetic diversity study by AFLP markersrdquoElectronic Journal of Biotechnology vol 9 no 4 pp 456ndash4602006
[68] M Zhong J CMcCarty J N Jenkins and S Saha ldquoAssessmentof day-neutral backcross populations of cotton using AFLPmarkersrdquo Journal of Cotton Science vol 6 no 2 pp 97ndash1032002
[69] A Rakshit S Rakshit J Singh et al ldquoAssociation of AFLPand SSR markers with agronomic and fibre quality traits inGossypium hirsutum Lrdquo Journal of Genetics vol 89 no 2 pp155ndash162 2010
[70] A Badigannavar and G Myers ldquoGenetic analysis of AFLPmarkers associated with seed quality traits in upland cotton(Gossypium hirsutum)rdquo in Beltwide Cotton Conferences NewOrleans La USA 2010
[71] M K Altaf J M C D Stewart M K Wajahatullah J Zhangand R G Cantrell ldquoMolecular and morphological geneticsof a trispecies F2 population of cottonrdquo in Proceedings of theBeltwide Cotton Conferences vol 1 pp 448ndash452 New OrleansLa USA January 1997
[72] M K Rana and K V Bhat ldquoA comparison of AFLP andRAPD markers for genetic diversity and cultivar identificationin cottonrdquo Journal of Plant Biochemistry and Biotechnology vol13 no 1 pp 19ndash24 2004
[73] J-M Lacape T-B Nguyen S Thibivilliers et al ldquoA combinedRFLP-SSR-AFLP map of tetraploid cotton based on a Gossyp-ium hirsutum times Gossypium barbadense backcross populationrdquoGenome vol 46 no 4 pp 612ndash626 2003
[74] D TautzM Trick andG A Dover ldquoCryptic simplicity in DNAis amajor source of genetic variationrdquoNature vol 322 no 6080pp 652ndash656 1986
[75] S Saha J Wu J N Jenkins et al ldquoBreeding and genetics effectof chromosome substitutions from Gossypium barbadense L 3-79 into G hirsutum L TM-1 on agronomic and fiber traitsrdquoJournal of Cotton Science vol 8 no 3 pp 162ndash169 2004
[76] O U K Reddy A E Pepper I Abdurakhmonov et al ldquoNewdinucleotide and trinucleotide microsatellite marker resourcesfor cotton genome researchrdquo Journal of Cotton Science vol 5no 2 pp 103ndash113 2001
[77] T B Nguyen M Giband P Brottier A M Risterucci and JM Lascape ldquoWide coverage of the tetraploid cotton genomeusing newly developed microsatellite markersrdquoTheoretical andApplied Genetics vol 109 no 1 pp 167ndash175 2004
12 The Scientific World Journal
[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
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Microbiology
6 The Scientific World Journal
genetic diversity using RAPD markers during 90s Geneticdiversity of 16 elite homozygous genotypes obtained fromthe inter-specific hybridization was studied using 80 RAPDmarkers [23] RAPD markers were used to differentiate theG hirsutum lines from the G arboretum [113] Similarly25 short duration genotypes of cotton were analyzed usingarbitrary primers [114] Later [115] studied genetic diversityof 31 Gossypium species 3 subspecies and 1 interspecifichybrid using 45 RAPD primers and the results showed thatgenetic relationship of many species is related to the centerof origin Recently genetic diversity in 18 cotton genotypes ofPakistan studied by 5 RAPD primers showed that two diversegenotypes of cotton (CIM-240 and CIM-443) have resistanceagainst cotton leaf curl virus [116]
AFLP technique was also used to distinguish the dif-ferences among diploid and tetraploid species of cotton byutilizing the variations in ribosomal RNA genes [106] Thegenetic diversity between the upland cotton wild species (Graimondii G thurberii and G sturtianum) and their BC
3
progenies was evaluated usingAFLPmarkers [117] Intra- andinterspecific relatedness of theG barbadense G arboreumGraimondii and G hirsutum are determined by AFLPs whichdemonstrated its usefulness for genetic relatedness acrosswide range of species [17] The relationship between the par-ents and four day neutral backcross generations of cotton wasdetermined using 43 AFLP markers [68] Comparative studywas conducted to evaluate AFLP and RAPD techniques using16 diploid cotton genotypes and it was concluded that AFLPmarkers are more efficient for polymorphism detection andfor analyzing of genetic diversity as compared to RAPDs [72]Similarly genetic diversity of 26 Tanzanian cotton genotypes(Gossypiumhirsutum L) was studied using theAFLPmarkers[66] The results of this study indicated the high values ofgenetic similarity which show the lower genetic diversityamong Tanzanian cotton cultivars Reference [65] mapped98 AFLP markers and assigned 22 distinctive chromoso-mal positions using cytogenetic deletion stocks Mappinginformation enhanced the utilization of AFLPs and can beused to saturate the existing marker frequency over differentchromosomes
In cotton SSRs are considered as a new class of DNAmarkers which hastened cotton genetic diversity and map-ping studies [27] and are important source to observe thetranscribed genes [118] There are multiple reports aboutusing the SSR markers for genetic diversity Reference [119]identified 71 SSR loci with 65 primer pairs and placed themondistinctive chromosomes of cotton Genetic diversity amongUS and Australian cultivars and day neutral lines of Ghirsutum was also analyzed by SSR markers [120]
Further saturation of SSR markers was extended by addi-tion of 204 markers which exhibited 261 segregating bandsgiving rise to 233 mapped loci in cotton [77] Interspecificpolymorphism between G barbadense and G hirsutum wasalso studied using SSR markers and results showed thatpolymorphism between species was high but it was lowwithin species [121] Reference [122] developed new SSRmarkers analyzed the status of 23 chromosomes and foundthat the inter loci distance was 49 cM Diversity among52 different G hirsutum cultivars was studied by 31 SSR
primer pairs and successfully discriminated the 52 cultivarsthrough broader allelic coverage [123] Similarly geneticdiversity of 43 upland cotton varieties [124] 56 sea-islandcotton accessions [125] 19 Bt cotton genotypes [107] 50representative Pakistani genotypes [104] and 193 uplandcotton cultivars [126] were evaluated using 36 237 104 70and 448 SSR markers respectively SSRs have also been usedto assess the genetic purity of the cotton hybrids [127] anddemonstrated as an effective tool for hybrid identification
Recent developments in next generation sequencing(NGS) and RNA-seq technology have generated high-throughput sequence data which facilitated the identificationof SNPs as effective and highly saturated markers for geneticstudies in cotton Genetic variations within and betweenthe different species of cotton have been characterized by1000 SNPs and 279 In-Dels from the 270 and 92 locisegregating in G barbadense and G hirsutum to providemapped molecular markers for crosses within species andintrogression of foreign germplasm in cotton [99] A genomereduction experiment based on the restriction site conserva-tion (GR-RSC) and previously generated assembly of expresssequence tags (ESTs) were used to discover the SNPs in 4accessions of G hirsutum and G barbadense A total 11834and 1679 non-genic and 4327 genic SNPs were identified inthe GR-RSC and EST assemblies using highly conservationparameters The KASPer assays were used to target the 1052(704 nongenic and 348 genic) genome specific SNPs betweenthe G hirsutum accessions [93] The assay then tested forthe Mendelian segregation ratio in the F
2population derived
from a cross of upland cotton (G hirsutum) cultivars
32 QTLs Mapping for Important Economic Traits in Cot-ton The regions in genomes to have genes linked with aquantitative trait are known as quantitative trait loci QTLs[128] and the process of developing linkage maps andperforming QTL analysis is referred to as QTLmapping [129130] QTL analysis stands on the principal of identifying aconnection among phenotype and genotype ofmarkers [128]The QTLs identified in cotton germplasm using differentmarker technologies are summarized in Table 3
RFLPs have been widely used to map genes of economicinterest in cotton Previously RFLP map of G hirsutum andG barbadensewas used tomap 14QTLs for fiber related traits[131] Similarly genes influencing density of stem and leaftrichomes [132] high gossypol plant and low seed gossypolcontents [117] were confined by RFLP markers Reference[131] developed an RFLP map of 261 markers distributedamong 26 linkage groups using F
2plants from an interspecific
cross Another genetic linkage map was developed usingRFLP markers and 26 QTLs were recognized for agronomicand fiber quality traits [41] Later on RFLP based QTLmapping was extended to leaf chlorophyll contents [133]Backcross population of G hirsutum and G barbadense wasused to map 28 9 and 8 QTLs for fiber length lengthuniformity and short fiber contents respectively using the262 RFLP markers [134]
RAPDs have also been widely used for QTL mappingin cotton however lack of reproducibility and unknown
The Scientific World Journal 7
Table3Anoverview
ofQTL
studies
incotto
n
Traits
Descriptor
Popu
latio
nSize
Marker(nu
mbera
ndtype)
QTL
snum
ber
Reference
Fiberq
uality
FSFLandFF
F 2171
RFLP
sand
85RA
PDs
13[135]
FSF 2
186
217SSRs800
RAPD
sUBC
and1040
OPE
RON
2[153]
LYLPSW
NSUQSFFL
FE
FTFFandIF
F 2120
144AFL
PsR
FLPs
and150SSRs
28[14
1]FS
FE
FLFU
LPandFF
F 2117
290SSRs
and9AFL
Ps16
[19]
FFBC
3F2
3662
262RF
LPs
41[185]
FLFLU
andSFC
BC3F
23662
262RF
LPs
45[134]
FSFE
FUFLandFF
RILrsquos
270
7508
SSRs384
SRAPs
and740IT-ISJs
13[186]
FLFSFF
andFE
F 2mdash
1378
SSRs
39[136]
FSFLFFFMTFE
andSFI
RILrsquos
180
4106
SSRsA
FLPsR
APD
sand
SRAPs
48[187]
FEFLFS
FFandFU
CP172
16052SSRs
63[188]
Fibera
ndagrono
mical
SCYLYLPBW
SIFM
TPE
RWFWTFFFLFE
andFS
RILrsquos
188
141S
SRs
56[189]
Yield
andfib
er
FSFLFFFE
LPSINB
SCYandLY
RILrsquos
258
2131
SSRs
53[19
0]
NB
BWSILPLISC
YLYFLFS
FFFE
andFU
4WCandinbred
lines
280
6123
SSRs
andES
T-SSRs
31[138]
SCYLYN
BBW
LPSILIand
FBN
RILrsquos
andIF2
180
2675
EST-SSRs
111
[191]
PHFBN
BWLPLISILYFLFS
FE
FFandFU
Ghirsutum
accessions
81121S
SRs
180
[3]
LISILYSCY
NSB
andFS
F 269
834SSRs437
SRAPs107
RAPD
sand
16RE
MAPs
52[192]
Morph
ological
LBNOSL1L1W1L2
W2L3
andW3
F 2180
261R
FLPs
62[19
3]EM
F 2andF 3
mdash40
83SSRs
54[14
0]NFB
F 2251
1165SSRs
5[19
4]Plant
architectural
PHFBL
FBN
FBA
FBL
PHandNMUB
RILrsquos
180
2130
SSRs2
RAPD
sand
1SRA
P16
[137]
NB
numbero
fbollsperp
lantB
Wb
ollw
eightSIseedindexLP
lintp
ercentL
Ilin
tind
exSIseed
indexSC
Yseed
cotto
nyieldperp
lantLY
linty
ield
perp
lantF
Lfib
erleng
thF
Sfib
erstr
ength
FEfi
ber
elong
ation
FUfiberu
niform
ityratio
FY
fiber
yello
wnessFFfib
erfin
enessFM
Tfib
ermaturityP
Hplant
heightFBL
fruitbranch
leng
thFBN
fruitbranch
numberFB
Afruitbranch
angleFL
Ufiberlength
unifo
rmitySFC
sho
rtfib
ercontentFR
fiberreflectanceSW
seedweightNSnu
mbero
fseeds
perp
lantU
Qupp
erqu
artilelengthSFsho
rtfib
ercontentFT
fibertenacityIFim
maturefi
bercon
tentSFIsho
rtfib
erindexNSB
num
bero
fseeds
perb
ollEM
earlymaturityN
MUB
lowerm
iddleandup
sideb
olln
umberNFB
nod
etofirstfruitin
gbranchLBN
Olob
enum
bersSL1sub
lobe
numbero
nthem
ainlobeL1
main-lobe
leng
thW
1main-lobe
widthL2second
-lobe
leng
thW
2second
-lobe
widthL3third
-lobe
leng
thW
3third
-lobe
leng
thPER
perim
eterW
Fweightfi
tnessWT
wallthicknessFBL
PHratioof
fruit
branch
leng
thto
planth
eightRILrsquosrecom
binant
inbred
linesIF2immortalized
F2s4W
Cfour
way
crossCP
com
positec
rossand
BC3F
2=backcrossfam
ilies
8 The Scientific World Journal
chromosomal positions remained main disadvantages whichrestricted the use of RAPDs in advanced studies Refer-ence [135] used 85 RAPD markers and identified 13 QTLsassociated to the fiber quality in the F
2population derived
from the G hirsutum and G barbadense cross There arenumerous studies on using the RAPDs for QTL mappingalong with other molecular markers (Table 3) An extensiveSSR genotyping was conducted over F
2populations from 3
diverse upland cotton genotypes using 1378 markers and 39fiber related QTLs were identified [136] Recombinant inbredlines (RILs) are also important mapping populations andseveral QTLs related to plant architecture [137] yield [3] andfiber quality [19] have been identified in upland cotton usingRILs About 31QTLs linked to the yield and fiber quality traitsare detected bywide array of SSR and EST SSRmarkers (6123)in 4 way cross populations developed from the 4 inbred linesof G hirsutum [138] A genetic linkage map of the tetraploidcotton was developed using 1601 pairs of SSR and 247 SNPmarkers [139] The genetic map consisted of the 2072 locicovering 3380 cm of the cotton genome Two F
2populations
were generated by the crosses of upland cotton cultivars and4083 SSR markers were used for QTL analysis which detect54 QTLs linked to early maturity [140]
A total of 144 primer combinations of AFLPs and 150 ofSSRs were used to detect 28 QTLs related to the fiber traits[141] To know the significant threshold for the LR statisticspermutation tests were carried out afterwhich 7QTLs remainsignificant RIL lines developed from the intraspecific cross ofupland cotton are used to detect the 12 epistatic and 4 mainQTLs related to the plant architectural traits by 2130 SSR 2RAPD and 1 SRAP markers [137]
Conclusively huge arrays of QTLs have been identifiedusing multiple molecular marker technologies Descriptionof stable QTL from diverse generations common QTL fromvarious populations and homologous QTLs raises the infor-mation on the genetic base Information about distributionof important QTLs in the genome of cotton is very importantand promises the future strategy for marker assisted breed-ing Cotton Gen serves as an important database for suchinformation and currently this database has 988 QTLs for25 different traits (httpwwwcottongenorgdataqtl) whichcan be surveyed according to objectivity
33 Genome Wide Association Studies (GWAS) in CottonAssociation mapping also known as linkage disequilibrium(LD) mapping has appeared as a tool to determine thevariation in complex traits using historical and evolutionaryrecombination actions at the population level [142] In asso-ciation mapping nonstructured populations are phenotypedand genotyped to identify the trait associated with marker[143] This results into capture of wider recombination andhigher resolution mapping as compared to linkage mapping[144] The applications of association mapping for cottonassist extensive employment of natural genetic diversity con-served within the worldwide collections of cotton germplasm[145] as in other plant germplasm resources Turning theefforts of gene-tagging from biparental QTL mapping to LD-based association study promise the productive employment
of ex situ conserved genetic diversity of global germplasmresources of cotton [10] The cotton genome may need fewnumbers of markers for productive associating mappingof complex traits which is also reported for other crops[146] Regarding the tetraploid genome of cotton with atotal recombination length of about 5200 cm and an average400 kb per cm [22] the LD block sizes of sim5-6 cm distanceis sufficient to conduct an association mapping of differenttraits that would require a maximum of sim1000 polymorphicmarkers for successful and reliable associationmapping [147]Extent of genome-wide LD and association mapping offiber quality traits were reported using 95 SSR markers in285 exotic accessions of G hirsutum comprised of 208 lan-draces and 77 varieties [10] Similarly LD-based associationmapping was conducted for fiber quality traits in 335 Ghirsutum germplasm using 202 SSR markers [147] Progressin genome sequencing technology provides an opportunity toproduce large size genotypic data which supports associationmapping over QTL mapping and because of this associationmapping is becoming more common [148]
34 Marker Assisted Selection (MAS) in Cotton Markerassisted selection (MAS) is a procedure by which a phenotypeis selected on the basis of genotype of a marker [128]Selecting the plants in the segregating population that havethe suitable genes combinations is the important componentof plant breeding [149] Once the markers tightly linked tothe genes have been detected breeders may use particularDNA marker to identify the plants carry the genes [150]The effectiveness and cost of MAS are influenced by themarker technique therefore it must be selected carefully[151] During the past two decades RAPDs techniqueshave been used for MAS for getting the glanded plantsand glandless seeds in the interspecific population of Gsturtianum and other species [152] It was exposed that DNAmarkers connected to the major QTL (QTLFS1) for fiberstrength could be utilized inMAS to increase fiber strength ofcommercial varieties in segregating populations [153] SomeRAPD markers were developed into locus specific sequencecharacterized amplified region (SCAR) markers to screen theBC1F4upland cotton For example SCAR 1920marker for the
major fiber strength QTL was developed and has been usedfor selecting desirable genotypes [154] Screening of the SNPswhich aremapped on chromosome 10 recognized extra 3 SNPmarkers thatwere associatedwith blue disease resistance gene(Cbd) which were employed to efficiently characterize a traitallowing MAS for strong levels of blue disease resistance incotton breeding programs [155]
4 Cotton Draft Genome and Its Implication
The increasing information of DNA sequencing allows thediscovery of genes and molecular markers associated withdifferent traits opening new avenues for crop improvement[148] Sequencing of DNA promises to display the spectrumof diversity in the genus Gossypium The tetraploid cottonspecies (2119899 = 4119909 = 52) such as G hirsutum and G bar-
The Scientific World Journal 9
badense are thought to have developed by an allopoly-ploidization that happened nearly 1-2 million years ago inwhich a D-genome species is pollen parent and species of anA-genome is maternal parent [12 156] It is essential to havea basic awareness of the structure of the component genomesto understand the cultivated polyploid genomes their evo-lution and interaction between their subgenomes Towardthe long-term aim of characterizing the diversity amongcotton genomes the cotton geneticists have prioritized the Dgenome progenitor G raimondii for complete sequencing Graimondii has a sim880Mb genome [157] the smallest genomein the genus Gossypium at sim60 of the size of diploid A-genome and 40 of the tetraploids [158] A physical map ofG raimondii genome was assembled and several evidencesreferred that the G raimondii genome is composed of twodifferent qualitative components one that is gene-rich andanother that is repeat-rich [158] About 40976 protein codinggenes and 2355 syntenic blocks identified in the genome ofG raimondii [159] Similarly the sequencing and assemblingof G arboreum genome depicted that 685 of the genomeis covered by repetitive DNA sequences and about 41330protein-coding genes were predicted in the genome of Garboreum [160]
5 Future Prospects
Cotton is a major source of foreign exchange for manycountries around the globe therefore major focus remainsthe enhancement of yield and quality of fiber This challengecan be accomplished by introducing new alleles from wildspecies [161 162] and use of modern molecular technologieshelping in increasing genetic gain of economic traits In thisscenario it is believed that sequencing of the G raimondii[159] and G arboreum [160] draft genomes will facilitate thegene discovery of important traits These genome resourcescan also be used for discovery of high-throughput markerplatforms like Select SNP arrays These high-throughputDNAmarkers will be helpful in recognizing the cotton geno-types carrying desired characters and was successfully usednot only to study the genetic diversity but to develop linkagemaps and mapping agronomic traits [12 20] which arenecessary for acceleration of varietal development Althoughthe QTL mapping for the various traits that is fiber yieldand quality [131] drought tolerance [133] disease resistance[163 164] and pests resistance [165] have been accomplishedin cotton but these may not be helpful to clone causal genesdue to lower marker densities In general the choice of amolecular marker technique is based on reliability statisticalpower and level of polymorphisms Since their inventionthey are being continuously modified for improved utilityto solve many problems and to bring forth automationWhen these markers techniques reach a greater degree ofautomation then it will be suitable to use DNA markersdirecting to a new ldquoGreen Revolutionrdquo in the agriculturalworld
Presently the enormous development of more efficientDNAmarkers will go on in the future because they can serveas an important tool for the plant breeders and geneticists
to develop the cultivars of cotton that are demanded bythe society It has been proposed that SNPs marker willhave large influence on MAS and mapping studies in futuredue to high abundance and development of sophisticateddetection system [195] GBS will clearly become the markergenotyping platform in coming years So the development ofnovel markers such as GBS and SNPs and the accessibility ofmodern technologies such as DNA Chips and microarrayshasten genome mapping and subsequent gene discovery inthe cotton for efficient cotton varietal development
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgment
We are highly thankful to Dr Awais Rasheed (CIMMYTChina) for his valued inputs and comments
References
[1] USDA Cotton and Wool Year book Dataset 2011 httpusdamannlibcornelleduMannUsdaviewDocumentInfododocu-mentID=128
[2] K F Abdellatif Y A Khidr Y M Mansy M M Lawendey andY A Soliman ldquoMolecular diversity of Egyptian cotton (Gossyp-ium barbadense L) and its relation to varietal developmentrdquoJournal of Crop Science and Biotechnology vol 15 pp 93ndash992012
[3] T Zhang N Qian X Zhu et al ldquoVariations and transmissionof QTL alleles for yield and fiber qualities in upland cottoncultivars developed in Chinardquo PLoS ONE vol 8 no 2 ArticleID e57220 2013
[4] H J Kim and B A Triplett ldquoCotton fiber growth in plantaand in vitro Models for plant cell elongation and cell wallbiogenesisrdquo Plant Physiology vol 127 no 4 pp 1361ndash1366 2001
[5] Y-L Ruan D J Llewellyn and R T Furbank ldquoSuppressionof sucrose synthase gene expression represses cotton fiber cellinitiation elongation and seed developmentrdquo Plant Cell vol 15no 4 pp 952ndash964 2003
[6] Y-M Qin and Y-X Zhu ldquoHow cotton fibers elongate a tale oflinear cell-growth moderdquo Current Opinion in Plant Biology vol14 no 1 pp 106ndash111 2011
[7] P A Fryxell ldquoA revised taxonomic interpretation of GossypiumL (Malvaceae )rdquo Rheedea vol 2 pp 108ndash165 1992
[8] J O Beasley ldquoThe production of polyploids in gossypiumrdquoJournal of Heredity vol 31 no 1 pp 39ndash48 1940
[9] J E Endrizzi E L Turcotte and R J Kohel ldquoGenetics cytologyand evolution of Gossypiumrdquo Advances in Genetics vol 23 pp271ndash375 1985
[10] I Y Abdurakhmonov R J Kohel J Z Yu et al ldquoMoleculardiversity and associationmapping of fiber quality traits in exoticG hirsutum L germplasmrdquo Genomics vol 92 no 6 pp 478ndash487 2008
[11] J F Wendel and R C Cronn ldquoPolyploidy and the evolutionaryhistory of cottonrdquo Advances in Agronomy vol 78 pp 139ndash1862003
10 The Scientific World Journal
[12] Z J Chen B E Scheffler E Dennis et al ldquoToward sequencingcotton (Gossypium) genomesrdquo Plant Physiology vol 145 no 4pp 1303ndash1310 2007
[13] M J Iqbal O U K Reddy K M El-Zik and A E PepperldquoA genetic bottleneck in the lsquoevolution under domesticationrsquoof upland cotton Gossypium hirsutum L examined using DNAfingerprintingrdquoTheoretical and Applied Genetics vol 103 no 4pp 547ndash554 2001
[14] J O Beasley ldquoThe origin of American tetraploid GossypiumspeciesrdquoThe American Naturalist vol 74 pp 285ndash286 1940
[15] J O Beasley ldquoMeiotic chromosome behavior in species specieshybrids haploids and induced polyploids ofGossypiumrdquoGenet-ics vol 27 no 1 pp 25ndash54 1942
[16] J F Wendel C L Brubaker and A E Percival ldquoGeneticdiversity in Gossypium hirsutum and the origin of uplandcottonrdquoAmerican Journal of Botany vol 79 no 11 pp 1291ndash13101992
[17] A M Abdalla O U K Reddy K M El-Zik and A E PepperldquoGenetic diversity and relationships of diploid and tetraploidcottons revealed using AFLPrdquoTheoretical and Applied Geneticsvol 102 no 2-3 pp 222ndash229 2001
[18] X L Song X Z Sun T Z Zhang and H G Wang ldquoAdvanceson genetic diversity of cotton (Gossypium)rdquo Acta BotanicaBoreali-Occidentalia Sinica vol 24 pp 2393ndash2397 2004
[19] Z-S Zhang Y-H XiaoM Luo et al ldquoConstruction of a geneticlinkage map and QTL analysis of fiber-related traits in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 144 no 1-2 pp91ndash99 2005
[20] H-B Zhang Y Li BWang andPWChee ldquoRecent advances incotton genomicsrdquo International Journal of Plant Genomics vol2008 Article ID 742304 20 pages 2008
[21] K Arumuganathan and E D Earle ldquoNuclear DNA contentof some important plant speciesrdquo Plant Molecular BiologyReporter vol 9 no 3 pp 208ndash218 1991
[22] A H Paterson and R H Smith ldquoFuture horizons biotech-nology of cotton improvementrdquo in Cotton Origin HistoryTechnology and Production pp 415ndash432 John Wiley amp SonsNew York NY USA 1999
[23] V Tatineni R G Cantrell and D D Davis ldquoGenetic diversityin elite cotton germplasm determined by morphological char-acteristics and RAPDsrdquo Crop Science vol 36 no 1 pp 186ndash1921996
[24] C L Brubaker and J F Wendel ldquoRFLP diversity in cottonrdquo inGenetic Improvement of Cotton Emerging Technologies pp 81ndash101 Science Publishers Enfield NH USA 2001
[25] N D Young ldquoConstructing a plant genetic linkage map withDNA markersrdquo in DNA-Based Markers in Plants pp 39ndash57 Kluwer Academic Publishers Dordrecht The Netherlands1994
[26] M Agarwal N Shrivastava andH Padh ldquoAdvances inmolecu-lar marker techniques and their applications in plant sciencesrdquoPlant Cell Reports vol 27 no 4 pp 617ndash631 2008
[27] S Preetha and T S Raveendren ldquoMolecular marker technologyin cottonrdquo Biotechnology and Molecular Biology Reviews vol 3no 2 pp 32ndash45 2008
[28] J R Andersen and T Lubberstedt ldquoFunctional markers inplantsrdquo Trends in Plant Science vol 8 no 11 pp 554ndash560 2003
[29] R K Kalia M K Rai S Kalia R Singh and A K DhawanldquoMicrosatellite markers an overview of the recent progress inplantsrdquo Euphytica vol 177 no 3 pp 309ndash334 2011
[30] N Appleby D Edwards and J Batley ldquoNew technologiesfor ultra-high throughput genotyping in plantsrdquo Methods inMolecular Biology vol 513 pp 19ndash39 2009
[31] Q H Xu X L Zhang and Y C Nie ldquoGenetic diversityevaluation of cultivars (G hirsumtum L) from the Changjiangriver valley and Tellow river valley by RAPD markersrdquo ActaGenetica Sinica vol 28 no 7 pp 683ndash690 2001
[32] H J Lu and G O Myers ldquoGenetic relationships and discrim-ination of ten influential upland cotton varieties using RAPDmarkersrdquoTheoretical and Applied Genetics vol 105 no 2-3 pp325ndash331 2002
[33] I Alvarez and J F Wendel ldquoCryptic interspecific introgressionand genetic differentiation within Gossypium aridum (Mal-vaceae) and its relativesrdquo Evolution vol 60 no 3 pp 505ndash5172006
[34] S Liu RGCantrell J CMcCarty Jr and JM Stewart ldquoSimplesequence repeat-based assessment of genetic diversity in cottonrace stock accessionsrdquoCrop Science vol 40 no 5 pp 1459ndash14692000
[35] L F Zhu X L Zhang and Y C Nie ldquoAnalysis of geneticdiversity in upland cotton (Gossypium hirsutum L) cultivarsfrom China and foreign countries by RAPDs and SSRsrdquo Journalof Agricultural Biotechnology vol 11 pp 450ndash455 2003
[36] M P Reddy N Sarla and E A Siddiq ldquoInter simple sequencerepeat (ISSR) polymorphism and its application in plant breed-ingrdquo Euphytica vol 128 no 1 pp 9ndash17 2002
[37] C Schlotterer ldquoThe evolution of molecular markersmdashjust amatter of fashionrdquo Nature Reviews Genetics vol 5 no 1 pp63ndash69 2004
[38] C L Brubaker and J F Wendel ldquoReevaluating the origin ofdomesticated cotton (Gossypium hirsutum Malvaceae) usingnuclear restriction fragment length polymorphisms (RFLPs)rdquoAmerican Journal of Botany vol 81 no 10 pp 1309ndash1326 1994
[39] Z H Yu Y H Park G R Lazo and R J KohelMolecularMap-ping of the Cotton Genome Agron Abstracts ASA MadisonWis USA 1997
[40] C L Brubaker A H Paterson and J F Wendel ldquoComparativegenetic mapping of allotetraploid cotton and its diploid progen-itorsrdquo Genome vol 42 no 2 pp 184ndash203 1999
[41] M Ulloa and W R Meredith Jr ldquoGenetic linkage map andQTL analysis of agronomic and fiber traits in an intraspecificpopulationrdquo Journal of Cotton Science vol 4 no 3 pp 161ndash1702000
[42] M Ulloa W R Meredith Jr Z W Shappley and A L KahlerldquoRFLP genetic linkage maps from four F
23populations and
a joinmap of Gossypium hirsutum Lrdquo Theoretical and AppliedGenetics vol 104 no 2-3 pp 200ndash208 2002
[43] A J Reinisch J-M Dong C L Brubaker D M Stelly J FWendel and A H Paterson ldquoA detailed RFLP map of cottonGossypium hirsutum x Gossypium barbadense chromosomeorganization and evolution in a disomic polyploid genomerdquoGenetics vol 138 no 3 pp 829ndash847 1994
[44] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoD-subgenome bias of Xcm resistance genes in tetraploidGossypium (cotton) suggests that polyploid formation hascreated novel avenues for evolutionrdquo Genetics vol 149 no 4pp 1987ndash1996 1998
[45] H A Erlich PCR Technology Principles and Applications forDNA Amplification W H Freeman New York NY USA 1991
[46] J G KWilliams A R Kubelik K J Livak J A Rafalski and SV Tingey ldquoDNApolymorphisms amplified by arbitrary primers
The Scientific World Journal 11
are useful as geneticmarkersrdquoNucleic Acids Research vol 18 no22 pp 6531ndash6535 1990
[47] S Khanam A Sham J L Bennetzen and M A M Aly ldquoAnal-ysis of molecular marker-based characterization and geneticvariation in date palm (Phoenix Dactylifera L)rdquo AustralianJournal of Crop Science vol 6 no 8 pp 1236ndash1244 2012
[48] K J Chalmers R Waugh J I Sprent A J Simons and WPowell ldquoDetection of genetic variation between and withinpopulations of Gliricidia sepium and G maculata using RAPDmarkersrdquo Heredity vol 69 pp 465ndash472 1992
[49] D S Multani and B R Lyon ldquoGenetic fingerprinting ofAustralian cotton cultivars with RAPD markersrdquo Genome vol38 no 5 pp 1005ndash1008 1995
[50] M KWajahatullah and J M Stewart ldquoGenomic affinity amongGossypium subgenus Sturtia species by RAPD analysisrdquo inProceeding of the Beltwide Cotton Conference National CottonCouncil p 452 Memphis Tenn USA 1997
[51] C D Geng Z Z Gong J Q Huang and Z C ZhangldquoIdentification of difference between cotton cultivars (G hirsu-tum) using the RAPD methodrdquo Jiangsu Journal of AgriculturalSciences vol 11 no 4 pp 21ndash24 1995
[52] T H Lan C G Cook and A H Paterson ldquoIdentification of aRAPDmarker linked tomale fertility restoration gene in cotton(Gossypium hirsutum L)rdquo Journal of Agricultural Genomics vol1 pp 1ndash5 1999
[53] B Shu K Fenling Z Y Yao Z G Mei Z Q Yuan and W XGang ldquoGenetic diversity analysis of representative elite cottonvarieties in three main cotton regions in China by RAPD andits relation with agronomic characteristicsrdquo Scientia AgriculturaSinica vol 34 pp 597ndash603 2001
[54] M Ulloa R G Cantrell R G Percy E Zeiger and Z Lu ldquoQTLanalysis of stomatal conductance and relationship to lint yieldin an interspecific cottonrdquo Journal of Cotton Science vol 4 no1 pp 10ndash18 2000
[55] B Bornet and M Branchard ldquoNonanchored inter simplesequence repeat (ISSR)markers reproducible and specific toolsfor genome fingerprintingrdquo Plant Molecular Biology Reportervol 19 no 3 pp 209ndash215 2001
[56] T M Culley and A D Wolfe ldquoPopulation genetic structureof the cleistogamous plant species Viola pubescens Aiton (Vio-laceae) as indicated by allozyme and ISSR molecular markersrdquoHeredity vol 86 no 5 pp 545ndash556 2000
[57] J B Wang ldquoISSR markers and their applications in plantgeneticsrdquo Yi Chuan vol 24 no 5 pp 613ndash616 2002
[58] T Nagaoka and Y Ogihara ldquoApplicability of inter-simplesequence repeat polymorphisms inwheat for use asDNAmark-ers in comparison to RFLP and RAPDmarkersrdquoTheoretical andApplied Genetics vol 94 no 5 pp 597ndash602 1997
[59] M Z Galvan B Bornet P A Balatti and M BranchardldquoInter simple sequence repeat (ISSR) markers as a tool for theassessment of both genetic diversity and gene pool origin incommon bean (Phaseolus vulgaris L)rdquo Euphytica vol 132 no3 pp 297ndash301 2003
[60] A Shi S Kantartzi M Mmbaga and P Chen ldquoDevelopmentof ISSR PCR markers for diversity study in dogwood (Cornusspp)rdquo Agriculture and Biology Journal of North America vol 1pp 189ndash194 2010
[61] M W Blair O Panaud and S R McCouch ldquoInter-simplesequence repeat (ISSR) amplification for analysis of microsatel-litemotif frequency and fingerprinting in rice (Oryza sativa L)rdquoTheoretical and Applied Genetics vol 98 no 5 pp 780ndash7921999
[62] B Bornet C Muller F Paulus and M Branchard ldquoHighlyinformative nature of inter simple sequence repeat (ISSR)sequences amplified using tri- and tetra-nucleotide primersfrom DNA of cauliflower (Brassica oleracea var botrytis L)rdquoGenome vol 45 no 5 pp 890ndash896 2002
[63] M Sica G Gamba S Montieri L Gaudio and S AcetoldquoISSR markers show differentiation among Italian populationsofAsparagus acutifolius Lrdquo BMCGenetics vol 6 article 17 2005
[64] P Vos R Hogers M Bleeker et al ldquoAFLP a new technique forDNA fingerprintingrdquo Nucleic Acids Research vol 23 no 21 pp4407ndash4414 1995
[65] G O Myers B Jiang M W Akash A Badigannavar and SSaha ldquoChromosomal assignment of AFLP markers in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 165 no 2 pp391ndash399 2009
[66] K Lukonge L Hersalman and M T Labuschagne ldquoGeneticdiversity of tanzanian cotton revealed by AFLP analysisrdquo inProceedings of the African Crop Science Conference vol 8 pp773ndash776 2007
[67] N Murtaza ldquoCotton genetic diversity study by AFLP markersrdquoElectronic Journal of Biotechnology vol 9 no 4 pp 456ndash4602006
[68] M Zhong J CMcCarty J N Jenkins and S Saha ldquoAssessmentof day-neutral backcross populations of cotton using AFLPmarkersrdquo Journal of Cotton Science vol 6 no 2 pp 97ndash1032002
[69] A Rakshit S Rakshit J Singh et al ldquoAssociation of AFLPand SSR markers with agronomic and fibre quality traits inGossypium hirsutum Lrdquo Journal of Genetics vol 89 no 2 pp155ndash162 2010
[70] A Badigannavar and G Myers ldquoGenetic analysis of AFLPmarkers associated with seed quality traits in upland cotton(Gossypium hirsutum)rdquo in Beltwide Cotton Conferences NewOrleans La USA 2010
[71] M K Altaf J M C D Stewart M K Wajahatullah J Zhangand R G Cantrell ldquoMolecular and morphological geneticsof a trispecies F2 population of cottonrdquo in Proceedings of theBeltwide Cotton Conferences vol 1 pp 448ndash452 New OrleansLa USA January 1997
[72] M K Rana and K V Bhat ldquoA comparison of AFLP andRAPD markers for genetic diversity and cultivar identificationin cottonrdquo Journal of Plant Biochemistry and Biotechnology vol13 no 1 pp 19ndash24 2004
[73] J-M Lacape T-B Nguyen S Thibivilliers et al ldquoA combinedRFLP-SSR-AFLP map of tetraploid cotton based on a Gossyp-ium hirsutum times Gossypium barbadense backcross populationrdquoGenome vol 46 no 4 pp 612ndash626 2003
[74] D TautzM Trick andG A Dover ldquoCryptic simplicity in DNAis amajor source of genetic variationrdquoNature vol 322 no 6080pp 652ndash656 1986
[75] S Saha J Wu J N Jenkins et al ldquoBreeding and genetics effectof chromosome substitutions from Gossypium barbadense L 3-79 into G hirsutum L TM-1 on agronomic and fiber traitsrdquoJournal of Cotton Science vol 8 no 3 pp 162ndash169 2004
[76] O U K Reddy A E Pepper I Abdurakhmonov et al ldquoNewdinucleotide and trinucleotide microsatellite marker resourcesfor cotton genome researchrdquo Journal of Cotton Science vol 5no 2 pp 103ndash113 2001
[77] T B Nguyen M Giband P Brottier A M Risterucci and JM Lascape ldquoWide coverage of the tetraploid cotton genomeusing newly developed microsatellite markersrdquoTheoretical andApplied Genetics vol 109 no 1 pp 167ndash175 2004
12 The Scientific World Journal
[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
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The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
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International Journal of
Microbiology
The Scientific World Journal 7
Table3Anoverview
ofQTL
studies
incotto
n
Traits
Descriptor
Popu
latio
nSize
Marker(nu
mbera
ndtype)
QTL
snum
ber
Reference
Fiberq
uality
FSFLandFF
F 2171
RFLP
sand
85RA
PDs
13[135]
FSF 2
186
217SSRs800
RAPD
sUBC
and1040
OPE
RON
2[153]
LYLPSW
NSUQSFFL
FE
FTFFandIF
F 2120
144AFL
PsR
FLPs
and150SSRs
28[14
1]FS
FE
FLFU
LPandFF
F 2117
290SSRs
and9AFL
Ps16
[19]
FFBC
3F2
3662
262RF
LPs
41[185]
FLFLU
andSFC
BC3F
23662
262RF
LPs
45[134]
FSFE
FUFLandFF
RILrsquos
270
7508
SSRs384
SRAPs
and740IT-ISJs
13[186]
FLFSFF
andFE
F 2mdash
1378
SSRs
39[136]
FSFLFFFMTFE
andSFI
RILrsquos
180
4106
SSRsA
FLPsR
APD
sand
SRAPs
48[187]
FEFLFS
FFandFU
CP172
16052SSRs
63[188]
Fibera
ndagrono
mical
SCYLYLPBW
SIFM
TPE
RWFWTFFFLFE
andFS
RILrsquos
188
141S
SRs
56[189]
Yield
andfib
er
FSFLFFFE
LPSINB
SCYandLY
RILrsquos
258
2131
SSRs
53[19
0]
NB
BWSILPLISC
YLYFLFS
FFFE
andFU
4WCandinbred
lines
280
6123
SSRs
andES
T-SSRs
31[138]
SCYLYN
BBW
LPSILIand
FBN
RILrsquos
andIF2
180
2675
EST-SSRs
111
[191]
PHFBN
BWLPLISILYFLFS
FE
FFandFU
Ghirsutum
accessions
81121S
SRs
180
[3]
LISILYSCY
NSB
andFS
F 269
834SSRs437
SRAPs107
RAPD
sand
16RE
MAPs
52[192]
Morph
ological
LBNOSL1L1W1L2
W2L3
andW3
F 2180
261R
FLPs
62[19
3]EM
F 2andF 3
mdash40
83SSRs
54[14
0]NFB
F 2251
1165SSRs
5[19
4]Plant
architectural
PHFBL
FBN
FBA
FBL
PHandNMUB
RILrsquos
180
2130
SSRs2
RAPD
sand
1SRA
P16
[137]
NB
numbero
fbollsperp
lantB
Wb
ollw
eightSIseedindexLP
lintp
ercentL
Ilin
tind
exSIseed
indexSC
Yseed
cotto
nyieldperp
lantLY
linty
ield
perp
lantF
Lfib
erleng
thF
Sfib
erstr
ength
FEfi
ber
elong
ation
FUfiberu
niform
ityratio
FY
fiber
yello
wnessFFfib
erfin
enessFM
Tfib
ermaturityP
Hplant
heightFBL
fruitbranch
leng
thFBN
fruitbranch
numberFB
Afruitbranch
angleFL
Ufiberlength
unifo
rmitySFC
sho
rtfib
ercontentFR
fiberreflectanceSW
seedweightNSnu
mbero
fseeds
perp
lantU
Qupp
erqu
artilelengthSFsho
rtfib
ercontentFT
fibertenacityIFim
maturefi
bercon
tentSFIsho
rtfib
erindexNSB
num
bero
fseeds
perb
ollEM
earlymaturityN
MUB
lowerm
iddleandup
sideb
olln
umberNFB
nod
etofirstfruitin
gbranchLBN
Olob
enum
bersSL1sub
lobe
numbero
nthem
ainlobeL1
main-lobe
leng
thW
1main-lobe
widthL2second
-lobe
leng
thW
2second
-lobe
widthL3third
-lobe
leng
thW
3third
-lobe
leng
thPER
perim
eterW
Fweightfi
tnessWT
wallthicknessFBL
PHratioof
fruit
branch
leng
thto
planth
eightRILrsquosrecom
binant
inbred
linesIF2immortalized
F2s4W
Cfour
way
crossCP
com
positec
rossand
BC3F
2=backcrossfam
ilies
8 The Scientific World Journal
chromosomal positions remained main disadvantages whichrestricted the use of RAPDs in advanced studies Refer-ence [135] used 85 RAPD markers and identified 13 QTLsassociated to the fiber quality in the F
2population derived
from the G hirsutum and G barbadense cross There arenumerous studies on using the RAPDs for QTL mappingalong with other molecular markers (Table 3) An extensiveSSR genotyping was conducted over F
2populations from 3
diverse upland cotton genotypes using 1378 markers and 39fiber related QTLs were identified [136] Recombinant inbredlines (RILs) are also important mapping populations andseveral QTLs related to plant architecture [137] yield [3] andfiber quality [19] have been identified in upland cotton usingRILs About 31QTLs linked to the yield and fiber quality traitsare detected bywide array of SSR and EST SSRmarkers (6123)in 4 way cross populations developed from the 4 inbred linesof G hirsutum [138] A genetic linkage map of the tetraploidcotton was developed using 1601 pairs of SSR and 247 SNPmarkers [139] The genetic map consisted of the 2072 locicovering 3380 cm of the cotton genome Two F
2populations
were generated by the crosses of upland cotton cultivars and4083 SSR markers were used for QTL analysis which detect54 QTLs linked to early maturity [140]
A total of 144 primer combinations of AFLPs and 150 ofSSRs were used to detect 28 QTLs related to the fiber traits[141] To know the significant threshold for the LR statisticspermutation tests were carried out afterwhich 7QTLs remainsignificant RIL lines developed from the intraspecific cross ofupland cotton are used to detect the 12 epistatic and 4 mainQTLs related to the plant architectural traits by 2130 SSR 2RAPD and 1 SRAP markers [137]
Conclusively huge arrays of QTLs have been identifiedusing multiple molecular marker technologies Descriptionof stable QTL from diverse generations common QTL fromvarious populations and homologous QTLs raises the infor-mation on the genetic base Information about distributionof important QTLs in the genome of cotton is very importantand promises the future strategy for marker assisted breed-ing Cotton Gen serves as an important database for suchinformation and currently this database has 988 QTLs for25 different traits (httpwwwcottongenorgdataqtl) whichcan be surveyed according to objectivity
33 Genome Wide Association Studies (GWAS) in CottonAssociation mapping also known as linkage disequilibrium(LD) mapping has appeared as a tool to determine thevariation in complex traits using historical and evolutionaryrecombination actions at the population level [142] In asso-ciation mapping nonstructured populations are phenotypedand genotyped to identify the trait associated with marker[143] This results into capture of wider recombination andhigher resolution mapping as compared to linkage mapping[144] The applications of association mapping for cottonassist extensive employment of natural genetic diversity con-served within the worldwide collections of cotton germplasm[145] as in other plant germplasm resources Turning theefforts of gene-tagging from biparental QTL mapping to LD-based association study promise the productive employment
of ex situ conserved genetic diversity of global germplasmresources of cotton [10] The cotton genome may need fewnumbers of markers for productive associating mappingof complex traits which is also reported for other crops[146] Regarding the tetraploid genome of cotton with atotal recombination length of about 5200 cm and an average400 kb per cm [22] the LD block sizes of sim5-6 cm distanceis sufficient to conduct an association mapping of differenttraits that would require a maximum of sim1000 polymorphicmarkers for successful and reliable associationmapping [147]Extent of genome-wide LD and association mapping offiber quality traits were reported using 95 SSR markers in285 exotic accessions of G hirsutum comprised of 208 lan-draces and 77 varieties [10] Similarly LD-based associationmapping was conducted for fiber quality traits in 335 Ghirsutum germplasm using 202 SSR markers [147] Progressin genome sequencing technology provides an opportunity toproduce large size genotypic data which supports associationmapping over QTL mapping and because of this associationmapping is becoming more common [148]
34 Marker Assisted Selection (MAS) in Cotton Markerassisted selection (MAS) is a procedure by which a phenotypeis selected on the basis of genotype of a marker [128]Selecting the plants in the segregating population that havethe suitable genes combinations is the important componentof plant breeding [149] Once the markers tightly linked tothe genes have been detected breeders may use particularDNA marker to identify the plants carry the genes [150]The effectiveness and cost of MAS are influenced by themarker technique therefore it must be selected carefully[151] During the past two decades RAPDs techniqueshave been used for MAS for getting the glanded plantsand glandless seeds in the interspecific population of Gsturtianum and other species [152] It was exposed that DNAmarkers connected to the major QTL (QTLFS1) for fiberstrength could be utilized inMAS to increase fiber strength ofcommercial varieties in segregating populations [153] SomeRAPD markers were developed into locus specific sequencecharacterized amplified region (SCAR) markers to screen theBC1F4upland cotton For example SCAR 1920marker for the
major fiber strength QTL was developed and has been usedfor selecting desirable genotypes [154] Screening of the SNPswhich aremapped on chromosome 10 recognized extra 3 SNPmarkers thatwere associatedwith blue disease resistance gene(Cbd) which were employed to efficiently characterize a traitallowing MAS for strong levels of blue disease resistance incotton breeding programs [155]
4 Cotton Draft Genome and Its Implication
The increasing information of DNA sequencing allows thediscovery of genes and molecular markers associated withdifferent traits opening new avenues for crop improvement[148] Sequencing of DNA promises to display the spectrumof diversity in the genus Gossypium The tetraploid cottonspecies (2119899 = 4119909 = 52) such as G hirsutum and G bar-
The Scientific World Journal 9
badense are thought to have developed by an allopoly-ploidization that happened nearly 1-2 million years ago inwhich a D-genome species is pollen parent and species of anA-genome is maternal parent [12 156] It is essential to havea basic awareness of the structure of the component genomesto understand the cultivated polyploid genomes their evo-lution and interaction between their subgenomes Towardthe long-term aim of characterizing the diversity amongcotton genomes the cotton geneticists have prioritized the Dgenome progenitor G raimondii for complete sequencing Graimondii has a sim880Mb genome [157] the smallest genomein the genus Gossypium at sim60 of the size of diploid A-genome and 40 of the tetraploids [158] A physical map ofG raimondii genome was assembled and several evidencesreferred that the G raimondii genome is composed of twodifferent qualitative components one that is gene-rich andanother that is repeat-rich [158] About 40976 protein codinggenes and 2355 syntenic blocks identified in the genome ofG raimondii [159] Similarly the sequencing and assemblingof G arboreum genome depicted that 685 of the genomeis covered by repetitive DNA sequences and about 41330protein-coding genes were predicted in the genome of Garboreum [160]
5 Future Prospects
Cotton is a major source of foreign exchange for manycountries around the globe therefore major focus remainsthe enhancement of yield and quality of fiber This challengecan be accomplished by introducing new alleles from wildspecies [161 162] and use of modern molecular technologieshelping in increasing genetic gain of economic traits In thisscenario it is believed that sequencing of the G raimondii[159] and G arboreum [160] draft genomes will facilitate thegene discovery of important traits These genome resourcescan also be used for discovery of high-throughput markerplatforms like Select SNP arrays These high-throughputDNAmarkers will be helpful in recognizing the cotton geno-types carrying desired characters and was successfully usednot only to study the genetic diversity but to develop linkagemaps and mapping agronomic traits [12 20] which arenecessary for acceleration of varietal development Althoughthe QTL mapping for the various traits that is fiber yieldand quality [131] drought tolerance [133] disease resistance[163 164] and pests resistance [165] have been accomplishedin cotton but these may not be helpful to clone causal genesdue to lower marker densities In general the choice of amolecular marker technique is based on reliability statisticalpower and level of polymorphisms Since their inventionthey are being continuously modified for improved utilityto solve many problems and to bring forth automationWhen these markers techniques reach a greater degree ofautomation then it will be suitable to use DNA markersdirecting to a new ldquoGreen Revolutionrdquo in the agriculturalworld
Presently the enormous development of more efficientDNAmarkers will go on in the future because they can serveas an important tool for the plant breeders and geneticists
to develop the cultivars of cotton that are demanded bythe society It has been proposed that SNPs marker willhave large influence on MAS and mapping studies in futuredue to high abundance and development of sophisticateddetection system [195] GBS will clearly become the markergenotyping platform in coming years So the development ofnovel markers such as GBS and SNPs and the accessibility ofmodern technologies such as DNA Chips and microarrayshasten genome mapping and subsequent gene discovery inthe cotton for efficient cotton varietal development
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgment
We are highly thankful to Dr Awais Rasheed (CIMMYTChina) for his valued inputs and comments
References
[1] USDA Cotton and Wool Year book Dataset 2011 httpusdamannlibcornelleduMannUsdaviewDocumentInfododocu-mentID=128
[2] K F Abdellatif Y A Khidr Y M Mansy M M Lawendey andY A Soliman ldquoMolecular diversity of Egyptian cotton (Gossyp-ium barbadense L) and its relation to varietal developmentrdquoJournal of Crop Science and Biotechnology vol 15 pp 93ndash992012
[3] T Zhang N Qian X Zhu et al ldquoVariations and transmissionof QTL alleles for yield and fiber qualities in upland cottoncultivars developed in Chinardquo PLoS ONE vol 8 no 2 ArticleID e57220 2013
[4] H J Kim and B A Triplett ldquoCotton fiber growth in plantaand in vitro Models for plant cell elongation and cell wallbiogenesisrdquo Plant Physiology vol 127 no 4 pp 1361ndash1366 2001
[5] Y-L Ruan D J Llewellyn and R T Furbank ldquoSuppressionof sucrose synthase gene expression represses cotton fiber cellinitiation elongation and seed developmentrdquo Plant Cell vol 15no 4 pp 952ndash964 2003
[6] Y-M Qin and Y-X Zhu ldquoHow cotton fibers elongate a tale oflinear cell-growth moderdquo Current Opinion in Plant Biology vol14 no 1 pp 106ndash111 2011
[7] P A Fryxell ldquoA revised taxonomic interpretation of GossypiumL (Malvaceae )rdquo Rheedea vol 2 pp 108ndash165 1992
[8] J O Beasley ldquoThe production of polyploids in gossypiumrdquoJournal of Heredity vol 31 no 1 pp 39ndash48 1940
[9] J E Endrizzi E L Turcotte and R J Kohel ldquoGenetics cytologyand evolution of Gossypiumrdquo Advances in Genetics vol 23 pp271ndash375 1985
[10] I Y Abdurakhmonov R J Kohel J Z Yu et al ldquoMoleculardiversity and associationmapping of fiber quality traits in exoticG hirsutum L germplasmrdquo Genomics vol 92 no 6 pp 478ndash487 2008
[11] J F Wendel and R C Cronn ldquoPolyploidy and the evolutionaryhistory of cottonrdquo Advances in Agronomy vol 78 pp 139ndash1862003
10 The Scientific World Journal
[12] Z J Chen B E Scheffler E Dennis et al ldquoToward sequencingcotton (Gossypium) genomesrdquo Plant Physiology vol 145 no 4pp 1303ndash1310 2007
[13] M J Iqbal O U K Reddy K M El-Zik and A E PepperldquoA genetic bottleneck in the lsquoevolution under domesticationrsquoof upland cotton Gossypium hirsutum L examined using DNAfingerprintingrdquoTheoretical and Applied Genetics vol 103 no 4pp 547ndash554 2001
[14] J O Beasley ldquoThe origin of American tetraploid GossypiumspeciesrdquoThe American Naturalist vol 74 pp 285ndash286 1940
[15] J O Beasley ldquoMeiotic chromosome behavior in species specieshybrids haploids and induced polyploids ofGossypiumrdquoGenet-ics vol 27 no 1 pp 25ndash54 1942
[16] J F Wendel C L Brubaker and A E Percival ldquoGeneticdiversity in Gossypium hirsutum and the origin of uplandcottonrdquoAmerican Journal of Botany vol 79 no 11 pp 1291ndash13101992
[17] A M Abdalla O U K Reddy K M El-Zik and A E PepperldquoGenetic diversity and relationships of diploid and tetraploidcottons revealed using AFLPrdquoTheoretical and Applied Geneticsvol 102 no 2-3 pp 222ndash229 2001
[18] X L Song X Z Sun T Z Zhang and H G Wang ldquoAdvanceson genetic diversity of cotton (Gossypium)rdquo Acta BotanicaBoreali-Occidentalia Sinica vol 24 pp 2393ndash2397 2004
[19] Z-S Zhang Y-H XiaoM Luo et al ldquoConstruction of a geneticlinkage map and QTL analysis of fiber-related traits in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 144 no 1-2 pp91ndash99 2005
[20] H-B Zhang Y Li BWang andPWChee ldquoRecent advances incotton genomicsrdquo International Journal of Plant Genomics vol2008 Article ID 742304 20 pages 2008
[21] K Arumuganathan and E D Earle ldquoNuclear DNA contentof some important plant speciesrdquo Plant Molecular BiologyReporter vol 9 no 3 pp 208ndash218 1991
[22] A H Paterson and R H Smith ldquoFuture horizons biotech-nology of cotton improvementrdquo in Cotton Origin HistoryTechnology and Production pp 415ndash432 John Wiley amp SonsNew York NY USA 1999
[23] V Tatineni R G Cantrell and D D Davis ldquoGenetic diversityin elite cotton germplasm determined by morphological char-acteristics and RAPDsrdquo Crop Science vol 36 no 1 pp 186ndash1921996
[24] C L Brubaker and J F Wendel ldquoRFLP diversity in cottonrdquo inGenetic Improvement of Cotton Emerging Technologies pp 81ndash101 Science Publishers Enfield NH USA 2001
[25] N D Young ldquoConstructing a plant genetic linkage map withDNA markersrdquo in DNA-Based Markers in Plants pp 39ndash57 Kluwer Academic Publishers Dordrecht The Netherlands1994
[26] M Agarwal N Shrivastava andH Padh ldquoAdvances inmolecu-lar marker techniques and their applications in plant sciencesrdquoPlant Cell Reports vol 27 no 4 pp 617ndash631 2008
[27] S Preetha and T S Raveendren ldquoMolecular marker technologyin cottonrdquo Biotechnology and Molecular Biology Reviews vol 3no 2 pp 32ndash45 2008
[28] J R Andersen and T Lubberstedt ldquoFunctional markers inplantsrdquo Trends in Plant Science vol 8 no 11 pp 554ndash560 2003
[29] R K Kalia M K Rai S Kalia R Singh and A K DhawanldquoMicrosatellite markers an overview of the recent progress inplantsrdquo Euphytica vol 177 no 3 pp 309ndash334 2011
[30] N Appleby D Edwards and J Batley ldquoNew technologiesfor ultra-high throughput genotyping in plantsrdquo Methods inMolecular Biology vol 513 pp 19ndash39 2009
[31] Q H Xu X L Zhang and Y C Nie ldquoGenetic diversityevaluation of cultivars (G hirsumtum L) from the Changjiangriver valley and Tellow river valley by RAPD markersrdquo ActaGenetica Sinica vol 28 no 7 pp 683ndash690 2001
[32] H J Lu and G O Myers ldquoGenetic relationships and discrim-ination of ten influential upland cotton varieties using RAPDmarkersrdquoTheoretical and Applied Genetics vol 105 no 2-3 pp325ndash331 2002
[33] I Alvarez and J F Wendel ldquoCryptic interspecific introgressionand genetic differentiation within Gossypium aridum (Mal-vaceae) and its relativesrdquo Evolution vol 60 no 3 pp 505ndash5172006
[34] S Liu RGCantrell J CMcCarty Jr and JM Stewart ldquoSimplesequence repeat-based assessment of genetic diversity in cottonrace stock accessionsrdquoCrop Science vol 40 no 5 pp 1459ndash14692000
[35] L F Zhu X L Zhang and Y C Nie ldquoAnalysis of geneticdiversity in upland cotton (Gossypium hirsutum L) cultivarsfrom China and foreign countries by RAPDs and SSRsrdquo Journalof Agricultural Biotechnology vol 11 pp 450ndash455 2003
[36] M P Reddy N Sarla and E A Siddiq ldquoInter simple sequencerepeat (ISSR) polymorphism and its application in plant breed-ingrdquo Euphytica vol 128 no 1 pp 9ndash17 2002
[37] C Schlotterer ldquoThe evolution of molecular markersmdashjust amatter of fashionrdquo Nature Reviews Genetics vol 5 no 1 pp63ndash69 2004
[38] C L Brubaker and J F Wendel ldquoReevaluating the origin ofdomesticated cotton (Gossypium hirsutum Malvaceae) usingnuclear restriction fragment length polymorphisms (RFLPs)rdquoAmerican Journal of Botany vol 81 no 10 pp 1309ndash1326 1994
[39] Z H Yu Y H Park G R Lazo and R J KohelMolecularMap-ping of the Cotton Genome Agron Abstracts ASA MadisonWis USA 1997
[40] C L Brubaker A H Paterson and J F Wendel ldquoComparativegenetic mapping of allotetraploid cotton and its diploid progen-itorsrdquo Genome vol 42 no 2 pp 184ndash203 1999
[41] M Ulloa and W R Meredith Jr ldquoGenetic linkage map andQTL analysis of agronomic and fiber traits in an intraspecificpopulationrdquo Journal of Cotton Science vol 4 no 3 pp 161ndash1702000
[42] M Ulloa W R Meredith Jr Z W Shappley and A L KahlerldquoRFLP genetic linkage maps from four F
23populations and
a joinmap of Gossypium hirsutum Lrdquo Theoretical and AppliedGenetics vol 104 no 2-3 pp 200ndash208 2002
[43] A J Reinisch J-M Dong C L Brubaker D M Stelly J FWendel and A H Paterson ldquoA detailed RFLP map of cottonGossypium hirsutum x Gossypium barbadense chromosomeorganization and evolution in a disomic polyploid genomerdquoGenetics vol 138 no 3 pp 829ndash847 1994
[44] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoD-subgenome bias of Xcm resistance genes in tetraploidGossypium (cotton) suggests that polyploid formation hascreated novel avenues for evolutionrdquo Genetics vol 149 no 4pp 1987ndash1996 1998
[45] H A Erlich PCR Technology Principles and Applications forDNA Amplification W H Freeman New York NY USA 1991
[46] J G KWilliams A R Kubelik K J Livak J A Rafalski and SV Tingey ldquoDNApolymorphisms amplified by arbitrary primers
The Scientific World Journal 11
are useful as geneticmarkersrdquoNucleic Acids Research vol 18 no22 pp 6531ndash6535 1990
[47] S Khanam A Sham J L Bennetzen and M A M Aly ldquoAnal-ysis of molecular marker-based characterization and geneticvariation in date palm (Phoenix Dactylifera L)rdquo AustralianJournal of Crop Science vol 6 no 8 pp 1236ndash1244 2012
[48] K J Chalmers R Waugh J I Sprent A J Simons and WPowell ldquoDetection of genetic variation between and withinpopulations of Gliricidia sepium and G maculata using RAPDmarkersrdquo Heredity vol 69 pp 465ndash472 1992
[49] D S Multani and B R Lyon ldquoGenetic fingerprinting ofAustralian cotton cultivars with RAPD markersrdquo Genome vol38 no 5 pp 1005ndash1008 1995
[50] M KWajahatullah and J M Stewart ldquoGenomic affinity amongGossypium subgenus Sturtia species by RAPD analysisrdquo inProceeding of the Beltwide Cotton Conference National CottonCouncil p 452 Memphis Tenn USA 1997
[51] C D Geng Z Z Gong J Q Huang and Z C ZhangldquoIdentification of difference between cotton cultivars (G hirsu-tum) using the RAPD methodrdquo Jiangsu Journal of AgriculturalSciences vol 11 no 4 pp 21ndash24 1995
[52] T H Lan C G Cook and A H Paterson ldquoIdentification of aRAPDmarker linked tomale fertility restoration gene in cotton(Gossypium hirsutum L)rdquo Journal of Agricultural Genomics vol1 pp 1ndash5 1999
[53] B Shu K Fenling Z Y Yao Z G Mei Z Q Yuan and W XGang ldquoGenetic diversity analysis of representative elite cottonvarieties in three main cotton regions in China by RAPD andits relation with agronomic characteristicsrdquo Scientia AgriculturaSinica vol 34 pp 597ndash603 2001
[54] M Ulloa R G Cantrell R G Percy E Zeiger and Z Lu ldquoQTLanalysis of stomatal conductance and relationship to lint yieldin an interspecific cottonrdquo Journal of Cotton Science vol 4 no1 pp 10ndash18 2000
[55] B Bornet and M Branchard ldquoNonanchored inter simplesequence repeat (ISSR)markers reproducible and specific toolsfor genome fingerprintingrdquo Plant Molecular Biology Reportervol 19 no 3 pp 209ndash215 2001
[56] T M Culley and A D Wolfe ldquoPopulation genetic structureof the cleistogamous plant species Viola pubescens Aiton (Vio-laceae) as indicated by allozyme and ISSR molecular markersrdquoHeredity vol 86 no 5 pp 545ndash556 2000
[57] J B Wang ldquoISSR markers and their applications in plantgeneticsrdquo Yi Chuan vol 24 no 5 pp 613ndash616 2002
[58] T Nagaoka and Y Ogihara ldquoApplicability of inter-simplesequence repeat polymorphisms inwheat for use asDNAmark-ers in comparison to RFLP and RAPDmarkersrdquoTheoretical andApplied Genetics vol 94 no 5 pp 597ndash602 1997
[59] M Z Galvan B Bornet P A Balatti and M BranchardldquoInter simple sequence repeat (ISSR) markers as a tool for theassessment of both genetic diversity and gene pool origin incommon bean (Phaseolus vulgaris L)rdquo Euphytica vol 132 no3 pp 297ndash301 2003
[60] A Shi S Kantartzi M Mmbaga and P Chen ldquoDevelopmentof ISSR PCR markers for diversity study in dogwood (Cornusspp)rdquo Agriculture and Biology Journal of North America vol 1pp 189ndash194 2010
[61] M W Blair O Panaud and S R McCouch ldquoInter-simplesequence repeat (ISSR) amplification for analysis of microsatel-litemotif frequency and fingerprinting in rice (Oryza sativa L)rdquoTheoretical and Applied Genetics vol 98 no 5 pp 780ndash7921999
[62] B Bornet C Muller F Paulus and M Branchard ldquoHighlyinformative nature of inter simple sequence repeat (ISSR)sequences amplified using tri- and tetra-nucleotide primersfrom DNA of cauliflower (Brassica oleracea var botrytis L)rdquoGenome vol 45 no 5 pp 890ndash896 2002
[63] M Sica G Gamba S Montieri L Gaudio and S AcetoldquoISSR markers show differentiation among Italian populationsofAsparagus acutifolius Lrdquo BMCGenetics vol 6 article 17 2005
[64] P Vos R Hogers M Bleeker et al ldquoAFLP a new technique forDNA fingerprintingrdquo Nucleic Acids Research vol 23 no 21 pp4407ndash4414 1995
[65] G O Myers B Jiang M W Akash A Badigannavar and SSaha ldquoChromosomal assignment of AFLP markers in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 165 no 2 pp391ndash399 2009
[66] K Lukonge L Hersalman and M T Labuschagne ldquoGeneticdiversity of tanzanian cotton revealed by AFLP analysisrdquo inProceedings of the African Crop Science Conference vol 8 pp773ndash776 2007
[67] N Murtaza ldquoCotton genetic diversity study by AFLP markersrdquoElectronic Journal of Biotechnology vol 9 no 4 pp 456ndash4602006
[68] M Zhong J CMcCarty J N Jenkins and S Saha ldquoAssessmentof day-neutral backcross populations of cotton using AFLPmarkersrdquo Journal of Cotton Science vol 6 no 2 pp 97ndash1032002
[69] A Rakshit S Rakshit J Singh et al ldquoAssociation of AFLPand SSR markers with agronomic and fibre quality traits inGossypium hirsutum Lrdquo Journal of Genetics vol 89 no 2 pp155ndash162 2010
[70] A Badigannavar and G Myers ldquoGenetic analysis of AFLPmarkers associated with seed quality traits in upland cotton(Gossypium hirsutum)rdquo in Beltwide Cotton Conferences NewOrleans La USA 2010
[71] M K Altaf J M C D Stewart M K Wajahatullah J Zhangand R G Cantrell ldquoMolecular and morphological geneticsof a trispecies F2 population of cottonrdquo in Proceedings of theBeltwide Cotton Conferences vol 1 pp 448ndash452 New OrleansLa USA January 1997
[72] M K Rana and K V Bhat ldquoA comparison of AFLP andRAPD markers for genetic diversity and cultivar identificationin cottonrdquo Journal of Plant Biochemistry and Biotechnology vol13 no 1 pp 19ndash24 2004
[73] J-M Lacape T-B Nguyen S Thibivilliers et al ldquoA combinedRFLP-SSR-AFLP map of tetraploid cotton based on a Gossyp-ium hirsutum times Gossypium barbadense backcross populationrdquoGenome vol 46 no 4 pp 612ndash626 2003
[74] D TautzM Trick andG A Dover ldquoCryptic simplicity in DNAis amajor source of genetic variationrdquoNature vol 322 no 6080pp 652ndash656 1986
[75] S Saha J Wu J N Jenkins et al ldquoBreeding and genetics effectof chromosome substitutions from Gossypium barbadense L 3-79 into G hirsutum L TM-1 on agronomic and fiber traitsrdquoJournal of Cotton Science vol 8 no 3 pp 162ndash169 2004
[76] O U K Reddy A E Pepper I Abdurakhmonov et al ldquoNewdinucleotide and trinucleotide microsatellite marker resourcesfor cotton genome researchrdquo Journal of Cotton Science vol 5no 2 pp 103ndash113 2001
[77] T B Nguyen M Giband P Brottier A M Risterucci and JM Lascape ldquoWide coverage of the tetraploid cotton genomeusing newly developed microsatellite markersrdquoTheoretical andApplied Genetics vol 109 no 1 pp 167ndash175 2004
12 The Scientific World Journal
[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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8 The Scientific World Journal
chromosomal positions remained main disadvantages whichrestricted the use of RAPDs in advanced studies Refer-ence [135] used 85 RAPD markers and identified 13 QTLsassociated to the fiber quality in the F
2population derived
from the G hirsutum and G barbadense cross There arenumerous studies on using the RAPDs for QTL mappingalong with other molecular markers (Table 3) An extensiveSSR genotyping was conducted over F
2populations from 3
diverse upland cotton genotypes using 1378 markers and 39fiber related QTLs were identified [136] Recombinant inbredlines (RILs) are also important mapping populations andseveral QTLs related to plant architecture [137] yield [3] andfiber quality [19] have been identified in upland cotton usingRILs About 31QTLs linked to the yield and fiber quality traitsare detected bywide array of SSR and EST SSRmarkers (6123)in 4 way cross populations developed from the 4 inbred linesof G hirsutum [138] A genetic linkage map of the tetraploidcotton was developed using 1601 pairs of SSR and 247 SNPmarkers [139] The genetic map consisted of the 2072 locicovering 3380 cm of the cotton genome Two F
2populations
were generated by the crosses of upland cotton cultivars and4083 SSR markers were used for QTL analysis which detect54 QTLs linked to early maturity [140]
A total of 144 primer combinations of AFLPs and 150 ofSSRs were used to detect 28 QTLs related to the fiber traits[141] To know the significant threshold for the LR statisticspermutation tests were carried out afterwhich 7QTLs remainsignificant RIL lines developed from the intraspecific cross ofupland cotton are used to detect the 12 epistatic and 4 mainQTLs related to the plant architectural traits by 2130 SSR 2RAPD and 1 SRAP markers [137]
Conclusively huge arrays of QTLs have been identifiedusing multiple molecular marker technologies Descriptionof stable QTL from diverse generations common QTL fromvarious populations and homologous QTLs raises the infor-mation on the genetic base Information about distributionof important QTLs in the genome of cotton is very importantand promises the future strategy for marker assisted breed-ing Cotton Gen serves as an important database for suchinformation and currently this database has 988 QTLs for25 different traits (httpwwwcottongenorgdataqtl) whichcan be surveyed according to objectivity
33 Genome Wide Association Studies (GWAS) in CottonAssociation mapping also known as linkage disequilibrium(LD) mapping has appeared as a tool to determine thevariation in complex traits using historical and evolutionaryrecombination actions at the population level [142] In asso-ciation mapping nonstructured populations are phenotypedand genotyped to identify the trait associated with marker[143] This results into capture of wider recombination andhigher resolution mapping as compared to linkage mapping[144] The applications of association mapping for cottonassist extensive employment of natural genetic diversity con-served within the worldwide collections of cotton germplasm[145] as in other plant germplasm resources Turning theefforts of gene-tagging from biparental QTL mapping to LD-based association study promise the productive employment
of ex situ conserved genetic diversity of global germplasmresources of cotton [10] The cotton genome may need fewnumbers of markers for productive associating mappingof complex traits which is also reported for other crops[146] Regarding the tetraploid genome of cotton with atotal recombination length of about 5200 cm and an average400 kb per cm [22] the LD block sizes of sim5-6 cm distanceis sufficient to conduct an association mapping of differenttraits that would require a maximum of sim1000 polymorphicmarkers for successful and reliable associationmapping [147]Extent of genome-wide LD and association mapping offiber quality traits were reported using 95 SSR markers in285 exotic accessions of G hirsutum comprised of 208 lan-draces and 77 varieties [10] Similarly LD-based associationmapping was conducted for fiber quality traits in 335 Ghirsutum germplasm using 202 SSR markers [147] Progressin genome sequencing technology provides an opportunity toproduce large size genotypic data which supports associationmapping over QTL mapping and because of this associationmapping is becoming more common [148]
34 Marker Assisted Selection (MAS) in Cotton Markerassisted selection (MAS) is a procedure by which a phenotypeis selected on the basis of genotype of a marker [128]Selecting the plants in the segregating population that havethe suitable genes combinations is the important componentof plant breeding [149] Once the markers tightly linked tothe genes have been detected breeders may use particularDNA marker to identify the plants carry the genes [150]The effectiveness and cost of MAS are influenced by themarker technique therefore it must be selected carefully[151] During the past two decades RAPDs techniqueshave been used for MAS for getting the glanded plantsand glandless seeds in the interspecific population of Gsturtianum and other species [152] It was exposed that DNAmarkers connected to the major QTL (QTLFS1) for fiberstrength could be utilized inMAS to increase fiber strength ofcommercial varieties in segregating populations [153] SomeRAPD markers were developed into locus specific sequencecharacterized amplified region (SCAR) markers to screen theBC1F4upland cotton For example SCAR 1920marker for the
major fiber strength QTL was developed and has been usedfor selecting desirable genotypes [154] Screening of the SNPswhich aremapped on chromosome 10 recognized extra 3 SNPmarkers thatwere associatedwith blue disease resistance gene(Cbd) which were employed to efficiently characterize a traitallowing MAS for strong levels of blue disease resistance incotton breeding programs [155]
4 Cotton Draft Genome and Its Implication
The increasing information of DNA sequencing allows thediscovery of genes and molecular markers associated withdifferent traits opening new avenues for crop improvement[148] Sequencing of DNA promises to display the spectrumof diversity in the genus Gossypium The tetraploid cottonspecies (2119899 = 4119909 = 52) such as G hirsutum and G bar-
The Scientific World Journal 9
badense are thought to have developed by an allopoly-ploidization that happened nearly 1-2 million years ago inwhich a D-genome species is pollen parent and species of anA-genome is maternal parent [12 156] It is essential to havea basic awareness of the structure of the component genomesto understand the cultivated polyploid genomes their evo-lution and interaction between their subgenomes Towardthe long-term aim of characterizing the diversity amongcotton genomes the cotton geneticists have prioritized the Dgenome progenitor G raimondii for complete sequencing Graimondii has a sim880Mb genome [157] the smallest genomein the genus Gossypium at sim60 of the size of diploid A-genome and 40 of the tetraploids [158] A physical map ofG raimondii genome was assembled and several evidencesreferred that the G raimondii genome is composed of twodifferent qualitative components one that is gene-rich andanother that is repeat-rich [158] About 40976 protein codinggenes and 2355 syntenic blocks identified in the genome ofG raimondii [159] Similarly the sequencing and assemblingof G arboreum genome depicted that 685 of the genomeis covered by repetitive DNA sequences and about 41330protein-coding genes were predicted in the genome of Garboreum [160]
5 Future Prospects
Cotton is a major source of foreign exchange for manycountries around the globe therefore major focus remainsthe enhancement of yield and quality of fiber This challengecan be accomplished by introducing new alleles from wildspecies [161 162] and use of modern molecular technologieshelping in increasing genetic gain of economic traits In thisscenario it is believed that sequencing of the G raimondii[159] and G arboreum [160] draft genomes will facilitate thegene discovery of important traits These genome resourcescan also be used for discovery of high-throughput markerplatforms like Select SNP arrays These high-throughputDNAmarkers will be helpful in recognizing the cotton geno-types carrying desired characters and was successfully usednot only to study the genetic diversity but to develop linkagemaps and mapping agronomic traits [12 20] which arenecessary for acceleration of varietal development Althoughthe QTL mapping for the various traits that is fiber yieldand quality [131] drought tolerance [133] disease resistance[163 164] and pests resistance [165] have been accomplishedin cotton but these may not be helpful to clone causal genesdue to lower marker densities In general the choice of amolecular marker technique is based on reliability statisticalpower and level of polymorphisms Since their inventionthey are being continuously modified for improved utilityto solve many problems and to bring forth automationWhen these markers techniques reach a greater degree ofautomation then it will be suitable to use DNA markersdirecting to a new ldquoGreen Revolutionrdquo in the agriculturalworld
Presently the enormous development of more efficientDNAmarkers will go on in the future because they can serveas an important tool for the plant breeders and geneticists
to develop the cultivars of cotton that are demanded bythe society It has been proposed that SNPs marker willhave large influence on MAS and mapping studies in futuredue to high abundance and development of sophisticateddetection system [195] GBS will clearly become the markergenotyping platform in coming years So the development ofnovel markers such as GBS and SNPs and the accessibility ofmodern technologies such as DNA Chips and microarrayshasten genome mapping and subsequent gene discovery inthe cotton for efficient cotton varietal development
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgment
We are highly thankful to Dr Awais Rasheed (CIMMYTChina) for his valued inputs and comments
References
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[2] K F Abdellatif Y A Khidr Y M Mansy M M Lawendey andY A Soliman ldquoMolecular diversity of Egyptian cotton (Gossyp-ium barbadense L) and its relation to varietal developmentrdquoJournal of Crop Science and Biotechnology vol 15 pp 93ndash992012
[3] T Zhang N Qian X Zhu et al ldquoVariations and transmissionof QTL alleles for yield and fiber qualities in upland cottoncultivars developed in Chinardquo PLoS ONE vol 8 no 2 ArticleID e57220 2013
[4] H J Kim and B A Triplett ldquoCotton fiber growth in plantaand in vitro Models for plant cell elongation and cell wallbiogenesisrdquo Plant Physiology vol 127 no 4 pp 1361ndash1366 2001
[5] Y-L Ruan D J Llewellyn and R T Furbank ldquoSuppressionof sucrose synthase gene expression represses cotton fiber cellinitiation elongation and seed developmentrdquo Plant Cell vol 15no 4 pp 952ndash964 2003
[6] Y-M Qin and Y-X Zhu ldquoHow cotton fibers elongate a tale oflinear cell-growth moderdquo Current Opinion in Plant Biology vol14 no 1 pp 106ndash111 2011
[7] P A Fryxell ldquoA revised taxonomic interpretation of GossypiumL (Malvaceae )rdquo Rheedea vol 2 pp 108ndash165 1992
[8] J O Beasley ldquoThe production of polyploids in gossypiumrdquoJournal of Heredity vol 31 no 1 pp 39ndash48 1940
[9] J E Endrizzi E L Turcotte and R J Kohel ldquoGenetics cytologyand evolution of Gossypiumrdquo Advances in Genetics vol 23 pp271ndash375 1985
[10] I Y Abdurakhmonov R J Kohel J Z Yu et al ldquoMoleculardiversity and associationmapping of fiber quality traits in exoticG hirsutum L germplasmrdquo Genomics vol 92 no 6 pp 478ndash487 2008
[11] J F Wendel and R C Cronn ldquoPolyploidy and the evolutionaryhistory of cottonrdquo Advances in Agronomy vol 78 pp 139ndash1862003
10 The Scientific World Journal
[12] Z J Chen B E Scheffler E Dennis et al ldquoToward sequencingcotton (Gossypium) genomesrdquo Plant Physiology vol 145 no 4pp 1303ndash1310 2007
[13] M J Iqbal O U K Reddy K M El-Zik and A E PepperldquoA genetic bottleneck in the lsquoevolution under domesticationrsquoof upland cotton Gossypium hirsutum L examined using DNAfingerprintingrdquoTheoretical and Applied Genetics vol 103 no 4pp 547ndash554 2001
[14] J O Beasley ldquoThe origin of American tetraploid GossypiumspeciesrdquoThe American Naturalist vol 74 pp 285ndash286 1940
[15] J O Beasley ldquoMeiotic chromosome behavior in species specieshybrids haploids and induced polyploids ofGossypiumrdquoGenet-ics vol 27 no 1 pp 25ndash54 1942
[16] J F Wendel C L Brubaker and A E Percival ldquoGeneticdiversity in Gossypium hirsutum and the origin of uplandcottonrdquoAmerican Journal of Botany vol 79 no 11 pp 1291ndash13101992
[17] A M Abdalla O U K Reddy K M El-Zik and A E PepperldquoGenetic diversity and relationships of diploid and tetraploidcottons revealed using AFLPrdquoTheoretical and Applied Geneticsvol 102 no 2-3 pp 222ndash229 2001
[18] X L Song X Z Sun T Z Zhang and H G Wang ldquoAdvanceson genetic diversity of cotton (Gossypium)rdquo Acta BotanicaBoreali-Occidentalia Sinica vol 24 pp 2393ndash2397 2004
[19] Z-S Zhang Y-H XiaoM Luo et al ldquoConstruction of a geneticlinkage map and QTL analysis of fiber-related traits in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 144 no 1-2 pp91ndash99 2005
[20] H-B Zhang Y Li BWang andPWChee ldquoRecent advances incotton genomicsrdquo International Journal of Plant Genomics vol2008 Article ID 742304 20 pages 2008
[21] K Arumuganathan and E D Earle ldquoNuclear DNA contentof some important plant speciesrdquo Plant Molecular BiologyReporter vol 9 no 3 pp 208ndash218 1991
[22] A H Paterson and R H Smith ldquoFuture horizons biotech-nology of cotton improvementrdquo in Cotton Origin HistoryTechnology and Production pp 415ndash432 John Wiley amp SonsNew York NY USA 1999
[23] V Tatineni R G Cantrell and D D Davis ldquoGenetic diversityin elite cotton germplasm determined by morphological char-acteristics and RAPDsrdquo Crop Science vol 36 no 1 pp 186ndash1921996
[24] C L Brubaker and J F Wendel ldquoRFLP diversity in cottonrdquo inGenetic Improvement of Cotton Emerging Technologies pp 81ndash101 Science Publishers Enfield NH USA 2001
[25] N D Young ldquoConstructing a plant genetic linkage map withDNA markersrdquo in DNA-Based Markers in Plants pp 39ndash57 Kluwer Academic Publishers Dordrecht The Netherlands1994
[26] M Agarwal N Shrivastava andH Padh ldquoAdvances inmolecu-lar marker techniques and their applications in plant sciencesrdquoPlant Cell Reports vol 27 no 4 pp 617ndash631 2008
[27] S Preetha and T S Raveendren ldquoMolecular marker technologyin cottonrdquo Biotechnology and Molecular Biology Reviews vol 3no 2 pp 32ndash45 2008
[28] J R Andersen and T Lubberstedt ldquoFunctional markers inplantsrdquo Trends in Plant Science vol 8 no 11 pp 554ndash560 2003
[29] R K Kalia M K Rai S Kalia R Singh and A K DhawanldquoMicrosatellite markers an overview of the recent progress inplantsrdquo Euphytica vol 177 no 3 pp 309ndash334 2011
[30] N Appleby D Edwards and J Batley ldquoNew technologiesfor ultra-high throughput genotyping in plantsrdquo Methods inMolecular Biology vol 513 pp 19ndash39 2009
[31] Q H Xu X L Zhang and Y C Nie ldquoGenetic diversityevaluation of cultivars (G hirsumtum L) from the Changjiangriver valley and Tellow river valley by RAPD markersrdquo ActaGenetica Sinica vol 28 no 7 pp 683ndash690 2001
[32] H J Lu and G O Myers ldquoGenetic relationships and discrim-ination of ten influential upland cotton varieties using RAPDmarkersrdquoTheoretical and Applied Genetics vol 105 no 2-3 pp325ndash331 2002
[33] I Alvarez and J F Wendel ldquoCryptic interspecific introgressionand genetic differentiation within Gossypium aridum (Mal-vaceae) and its relativesrdquo Evolution vol 60 no 3 pp 505ndash5172006
[34] S Liu RGCantrell J CMcCarty Jr and JM Stewart ldquoSimplesequence repeat-based assessment of genetic diversity in cottonrace stock accessionsrdquoCrop Science vol 40 no 5 pp 1459ndash14692000
[35] L F Zhu X L Zhang and Y C Nie ldquoAnalysis of geneticdiversity in upland cotton (Gossypium hirsutum L) cultivarsfrom China and foreign countries by RAPDs and SSRsrdquo Journalof Agricultural Biotechnology vol 11 pp 450ndash455 2003
[36] M P Reddy N Sarla and E A Siddiq ldquoInter simple sequencerepeat (ISSR) polymorphism and its application in plant breed-ingrdquo Euphytica vol 128 no 1 pp 9ndash17 2002
[37] C Schlotterer ldquoThe evolution of molecular markersmdashjust amatter of fashionrdquo Nature Reviews Genetics vol 5 no 1 pp63ndash69 2004
[38] C L Brubaker and J F Wendel ldquoReevaluating the origin ofdomesticated cotton (Gossypium hirsutum Malvaceae) usingnuclear restriction fragment length polymorphisms (RFLPs)rdquoAmerican Journal of Botany vol 81 no 10 pp 1309ndash1326 1994
[39] Z H Yu Y H Park G R Lazo and R J KohelMolecularMap-ping of the Cotton Genome Agron Abstracts ASA MadisonWis USA 1997
[40] C L Brubaker A H Paterson and J F Wendel ldquoComparativegenetic mapping of allotetraploid cotton and its diploid progen-itorsrdquo Genome vol 42 no 2 pp 184ndash203 1999
[41] M Ulloa and W R Meredith Jr ldquoGenetic linkage map andQTL analysis of agronomic and fiber traits in an intraspecificpopulationrdquo Journal of Cotton Science vol 4 no 3 pp 161ndash1702000
[42] M Ulloa W R Meredith Jr Z W Shappley and A L KahlerldquoRFLP genetic linkage maps from four F
23populations and
a joinmap of Gossypium hirsutum Lrdquo Theoretical and AppliedGenetics vol 104 no 2-3 pp 200ndash208 2002
[43] A J Reinisch J-M Dong C L Brubaker D M Stelly J FWendel and A H Paterson ldquoA detailed RFLP map of cottonGossypium hirsutum x Gossypium barbadense chromosomeorganization and evolution in a disomic polyploid genomerdquoGenetics vol 138 no 3 pp 829ndash847 1994
[44] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoD-subgenome bias of Xcm resistance genes in tetraploidGossypium (cotton) suggests that polyploid formation hascreated novel avenues for evolutionrdquo Genetics vol 149 no 4pp 1987ndash1996 1998
[45] H A Erlich PCR Technology Principles and Applications forDNA Amplification W H Freeman New York NY USA 1991
[46] J G KWilliams A R Kubelik K J Livak J A Rafalski and SV Tingey ldquoDNApolymorphisms amplified by arbitrary primers
The Scientific World Journal 11
are useful as geneticmarkersrdquoNucleic Acids Research vol 18 no22 pp 6531ndash6535 1990
[47] S Khanam A Sham J L Bennetzen and M A M Aly ldquoAnal-ysis of molecular marker-based characterization and geneticvariation in date palm (Phoenix Dactylifera L)rdquo AustralianJournal of Crop Science vol 6 no 8 pp 1236ndash1244 2012
[48] K J Chalmers R Waugh J I Sprent A J Simons and WPowell ldquoDetection of genetic variation between and withinpopulations of Gliricidia sepium and G maculata using RAPDmarkersrdquo Heredity vol 69 pp 465ndash472 1992
[49] D S Multani and B R Lyon ldquoGenetic fingerprinting ofAustralian cotton cultivars with RAPD markersrdquo Genome vol38 no 5 pp 1005ndash1008 1995
[50] M KWajahatullah and J M Stewart ldquoGenomic affinity amongGossypium subgenus Sturtia species by RAPD analysisrdquo inProceeding of the Beltwide Cotton Conference National CottonCouncil p 452 Memphis Tenn USA 1997
[51] C D Geng Z Z Gong J Q Huang and Z C ZhangldquoIdentification of difference between cotton cultivars (G hirsu-tum) using the RAPD methodrdquo Jiangsu Journal of AgriculturalSciences vol 11 no 4 pp 21ndash24 1995
[52] T H Lan C G Cook and A H Paterson ldquoIdentification of aRAPDmarker linked tomale fertility restoration gene in cotton(Gossypium hirsutum L)rdquo Journal of Agricultural Genomics vol1 pp 1ndash5 1999
[53] B Shu K Fenling Z Y Yao Z G Mei Z Q Yuan and W XGang ldquoGenetic diversity analysis of representative elite cottonvarieties in three main cotton regions in China by RAPD andits relation with agronomic characteristicsrdquo Scientia AgriculturaSinica vol 34 pp 597ndash603 2001
[54] M Ulloa R G Cantrell R G Percy E Zeiger and Z Lu ldquoQTLanalysis of stomatal conductance and relationship to lint yieldin an interspecific cottonrdquo Journal of Cotton Science vol 4 no1 pp 10ndash18 2000
[55] B Bornet and M Branchard ldquoNonanchored inter simplesequence repeat (ISSR)markers reproducible and specific toolsfor genome fingerprintingrdquo Plant Molecular Biology Reportervol 19 no 3 pp 209ndash215 2001
[56] T M Culley and A D Wolfe ldquoPopulation genetic structureof the cleistogamous plant species Viola pubescens Aiton (Vio-laceae) as indicated by allozyme and ISSR molecular markersrdquoHeredity vol 86 no 5 pp 545ndash556 2000
[57] J B Wang ldquoISSR markers and their applications in plantgeneticsrdquo Yi Chuan vol 24 no 5 pp 613ndash616 2002
[58] T Nagaoka and Y Ogihara ldquoApplicability of inter-simplesequence repeat polymorphisms inwheat for use asDNAmark-ers in comparison to RFLP and RAPDmarkersrdquoTheoretical andApplied Genetics vol 94 no 5 pp 597ndash602 1997
[59] M Z Galvan B Bornet P A Balatti and M BranchardldquoInter simple sequence repeat (ISSR) markers as a tool for theassessment of both genetic diversity and gene pool origin incommon bean (Phaseolus vulgaris L)rdquo Euphytica vol 132 no3 pp 297ndash301 2003
[60] A Shi S Kantartzi M Mmbaga and P Chen ldquoDevelopmentof ISSR PCR markers for diversity study in dogwood (Cornusspp)rdquo Agriculture and Biology Journal of North America vol 1pp 189ndash194 2010
[61] M W Blair O Panaud and S R McCouch ldquoInter-simplesequence repeat (ISSR) amplification for analysis of microsatel-litemotif frequency and fingerprinting in rice (Oryza sativa L)rdquoTheoretical and Applied Genetics vol 98 no 5 pp 780ndash7921999
[62] B Bornet C Muller F Paulus and M Branchard ldquoHighlyinformative nature of inter simple sequence repeat (ISSR)sequences amplified using tri- and tetra-nucleotide primersfrom DNA of cauliflower (Brassica oleracea var botrytis L)rdquoGenome vol 45 no 5 pp 890ndash896 2002
[63] M Sica G Gamba S Montieri L Gaudio and S AcetoldquoISSR markers show differentiation among Italian populationsofAsparagus acutifolius Lrdquo BMCGenetics vol 6 article 17 2005
[64] P Vos R Hogers M Bleeker et al ldquoAFLP a new technique forDNA fingerprintingrdquo Nucleic Acids Research vol 23 no 21 pp4407ndash4414 1995
[65] G O Myers B Jiang M W Akash A Badigannavar and SSaha ldquoChromosomal assignment of AFLP markers in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 165 no 2 pp391ndash399 2009
[66] K Lukonge L Hersalman and M T Labuschagne ldquoGeneticdiversity of tanzanian cotton revealed by AFLP analysisrdquo inProceedings of the African Crop Science Conference vol 8 pp773ndash776 2007
[67] N Murtaza ldquoCotton genetic diversity study by AFLP markersrdquoElectronic Journal of Biotechnology vol 9 no 4 pp 456ndash4602006
[68] M Zhong J CMcCarty J N Jenkins and S Saha ldquoAssessmentof day-neutral backcross populations of cotton using AFLPmarkersrdquo Journal of Cotton Science vol 6 no 2 pp 97ndash1032002
[69] A Rakshit S Rakshit J Singh et al ldquoAssociation of AFLPand SSR markers with agronomic and fibre quality traits inGossypium hirsutum Lrdquo Journal of Genetics vol 89 no 2 pp155ndash162 2010
[70] A Badigannavar and G Myers ldquoGenetic analysis of AFLPmarkers associated with seed quality traits in upland cotton(Gossypium hirsutum)rdquo in Beltwide Cotton Conferences NewOrleans La USA 2010
[71] M K Altaf J M C D Stewart M K Wajahatullah J Zhangand R G Cantrell ldquoMolecular and morphological geneticsof a trispecies F2 population of cottonrdquo in Proceedings of theBeltwide Cotton Conferences vol 1 pp 448ndash452 New OrleansLa USA January 1997
[72] M K Rana and K V Bhat ldquoA comparison of AFLP andRAPD markers for genetic diversity and cultivar identificationin cottonrdquo Journal of Plant Biochemistry and Biotechnology vol13 no 1 pp 19ndash24 2004
[73] J-M Lacape T-B Nguyen S Thibivilliers et al ldquoA combinedRFLP-SSR-AFLP map of tetraploid cotton based on a Gossyp-ium hirsutum times Gossypium barbadense backcross populationrdquoGenome vol 46 no 4 pp 612ndash626 2003
[74] D TautzM Trick andG A Dover ldquoCryptic simplicity in DNAis amajor source of genetic variationrdquoNature vol 322 no 6080pp 652ndash656 1986
[75] S Saha J Wu J N Jenkins et al ldquoBreeding and genetics effectof chromosome substitutions from Gossypium barbadense L 3-79 into G hirsutum L TM-1 on agronomic and fiber traitsrdquoJournal of Cotton Science vol 8 no 3 pp 162ndash169 2004
[76] O U K Reddy A E Pepper I Abdurakhmonov et al ldquoNewdinucleotide and trinucleotide microsatellite marker resourcesfor cotton genome researchrdquo Journal of Cotton Science vol 5no 2 pp 103ndash113 2001
[77] T B Nguyen M Giband P Brottier A M Risterucci and JM Lascape ldquoWide coverage of the tetraploid cotton genomeusing newly developed microsatellite markersrdquoTheoretical andApplied Genetics vol 109 no 1 pp 167ndash175 2004
12 The Scientific World Journal
[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
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Signal TransductionJournal of
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BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Genetics Research International
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Enzyme Research
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International Journal of
Microbiology
The Scientific World Journal 9
badense are thought to have developed by an allopoly-ploidization that happened nearly 1-2 million years ago inwhich a D-genome species is pollen parent and species of anA-genome is maternal parent [12 156] It is essential to havea basic awareness of the structure of the component genomesto understand the cultivated polyploid genomes their evo-lution and interaction between their subgenomes Towardthe long-term aim of characterizing the diversity amongcotton genomes the cotton geneticists have prioritized the Dgenome progenitor G raimondii for complete sequencing Graimondii has a sim880Mb genome [157] the smallest genomein the genus Gossypium at sim60 of the size of diploid A-genome and 40 of the tetraploids [158] A physical map ofG raimondii genome was assembled and several evidencesreferred that the G raimondii genome is composed of twodifferent qualitative components one that is gene-rich andanother that is repeat-rich [158] About 40976 protein codinggenes and 2355 syntenic blocks identified in the genome ofG raimondii [159] Similarly the sequencing and assemblingof G arboreum genome depicted that 685 of the genomeis covered by repetitive DNA sequences and about 41330protein-coding genes were predicted in the genome of Garboreum [160]
5 Future Prospects
Cotton is a major source of foreign exchange for manycountries around the globe therefore major focus remainsthe enhancement of yield and quality of fiber This challengecan be accomplished by introducing new alleles from wildspecies [161 162] and use of modern molecular technologieshelping in increasing genetic gain of economic traits In thisscenario it is believed that sequencing of the G raimondii[159] and G arboreum [160] draft genomes will facilitate thegene discovery of important traits These genome resourcescan also be used for discovery of high-throughput markerplatforms like Select SNP arrays These high-throughputDNAmarkers will be helpful in recognizing the cotton geno-types carrying desired characters and was successfully usednot only to study the genetic diversity but to develop linkagemaps and mapping agronomic traits [12 20] which arenecessary for acceleration of varietal development Althoughthe QTL mapping for the various traits that is fiber yieldand quality [131] drought tolerance [133] disease resistance[163 164] and pests resistance [165] have been accomplishedin cotton but these may not be helpful to clone causal genesdue to lower marker densities In general the choice of amolecular marker technique is based on reliability statisticalpower and level of polymorphisms Since their inventionthey are being continuously modified for improved utilityto solve many problems and to bring forth automationWhen these markers techniques reach a greater degree ofautomation then it will be suitable to use DNA markersdirecting to a new ldquoGreen Revolutionrdquo in the agriculturalworld
Presently the enormous development of more efficientDNAmarkers will go on in the future because they can serveas an important tool for the plant breeders and geneticists
to develop the cultivars of cotton that are demanded bythe society It has been proposed that SNPs marker willhave large influence on MAS and mapping studies in futuredue to high abundance and development of sophisticateddetection system [195] GBS will clearly become the markergenotyping platform in coming years So the development ofnovel markers such as GBS and SNPs and the accessibility ofmodern technologies such as DNA Chips and microarrayshasten genome mapping and subsequent gene discovery inthe cotton for efficient cotton varietal development
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgment
We are highly thankful to Dr Awais Rasheed (CIMMYTChina) for his valued inputs and comments
References
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[2] K F Abdellatif Y A Khidr Y M Mansy M M Lawendey andY A Soliman ldquoMolecular diversity of Egyptian cotton (Gossyp-ium barbadense L) and its relation to varietal developmentrdquoJournal of Crop Science and Biotechnology vol 15 pp 93ndash992012
[3] T Zhang N Qian X Zhu et al ldquoVariations and transmissionof QTL alleles for yield and fiber qualities in upland cottoncultivars developed in Chinardquo PLoS ONE vol 8 no 2 ArticleID e57220 2013
[4] H J Kim and B A Triplett ldquoCotton fiber growth in plantaand in vitro Models for plant cell elongation and cell wallbiogenesisrdquo Plant Physiology vol 127 no 4 pp 1361ndash1366 2001
[5] Y-L Ruan D J Llewellyn and R T Furbank ldquoSuppressionof sucrose synthase gene expression represses cotton fiber cellinitiation elongation and seed developmentrdquo Plant Cell vol 15no 4 pp 952ndash964 2003
[6] Y-M Qin and Y-X Zhu ldquoHow cotton fibers elongate a tale oflinear cell-growth moderdquo Current Opinion in Plant Biology vol14 no 1 pp 106ndash111 2011
[7] P A Fryxell ldquoA revised taxonomic interpretation of GossypiumL (Malvaceae )rdquo Rheedea vol 2 pp 108ndash165 1992
[8] J O Beasley ldquoThe production of polyploids in gossypiumrdquoJournal of Heredity vol 31 no 1 pp 39ndash48 1940
[9] J E Endrizzi E L Turcotte and R J Kohel ldquoGenetics cytologyand evolution of Gossypiumrdquo Advances in Genetics vol 23 pp271ndash375 1985
[10] I Y Abdurakhmonov R J Kohel J Z Yu et al ldquoMoleculardiversity and associationmapping of fiber quality traits in exoticG hirsutum L germplasmrdquo Genomics vol 92 no 6 pp 478ndash487 2008
[11] J F Wendel and R C Cronn ldquoPolyploidy and the evolutionaryhistory of cottonrdquo Advances in Agronomy vol 78 pp 139ndash1862003
10 The Scientific World Journal
[12] Z J Chen B E Scheffler E Dennis et al ldquoToward sequencingcotton (Gossypium) genomesrdquo Plant Physiology vol 145 no 4pp 1303ndash1310 2007
[13] M J Iqbal O U K Reddy K M El-Zik and A E PepperldquoA genetic bottleneck in the lsquoevolution under domesticationrsquoof upland cotton Gossypium hirsutum L examined using DNAfingerprintingrdquoTheoretical and Applied Genetics vol 103 no 4pp 547ndash554 2001
[14] J O Beasley ldquoThe origin of American tetraploid GossypiumspeciesrdquoThe American Naturalist vol 74 pp 285ndash286 1940
[15] J O Beasley ldquoMeiotic chromosome behavior in species specieshybrids haploids and induced polyploids ofGossypiumrdquoGenet-ics vol 27 no 1 pp 25ndash54 1942
[16] J F Wendel C L Brubaker and A E Percival ldquoGeneticdiversity in Gossypium hirsutum and the origin of uplandcottonrdquoAmerican Journal of Botany vol 79 no 11 pp 1291ndash13101992
[17] A M Abdalla O U K Reddy K M El-Zik and A E PepperldquoGenetic diversity and relationships of diploid and tetraploidcottons revealed using AFLPrdquoTheoretical and Applied Geneticsvol 102 no 2-3 pp 222ndash229 2001
[18] X L Song X Z Sun T Z Zhang and H G Wang ldquoAdvanceson genetic diversity of cotton (Gossypium)rdquo Acta BotanicaBoreali-Occidentalia Sinica vol 24 pp 2393ndash2397 2004
[19] Z-S Zhang Y-H XiaoM Luo et al ldquoConstruction of a geneticlinkage map and QTL analysis of fiber-related traits in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 144 no 1-2 pp91ndash99 2005
[20] H-B Zhang Y Li BWang andPWChee ldquoRecent advances incotton genomicsrdquo International Journal of Plant Genomics vol2008 Article ID 742304 20 pages 2008
[21] K Arumuganathan and E D Earle ldquoNuclear DNA contentof some important plant speciesrdquo Plant Molecular BiologyReporter vol 9 no 3 pp 208ndash218 1991
[22] A H Paterson and R H Smith ldquoFuture horizons biotech-nology of cotton improvementrdquo in Cotton Origin HistoryTechnology and Production pp 415ndash432 John Wiley amp SonsNew York NY USA 1999
[23] V Tatineni R G Cantrell and D D Davis ldquoGenetic diversityin elite cotton germplasm determined by morphological char-acteristics and RAPDsrdquo Crop Science vol 36 no 1 pp 186ndash1921996
[24] C L Brubaker and J F Wendel ldquoRFLP diversity in cottonrdquo inGenetic Improvement of Cotton Emerging Technologies pp 81ndash101 Science Publishers Enfield NH USA 2001
[25] N D Young ldquoConstructing a plant genetic linkage map withDNA markersrdquo in DNA-Based Markers in Plants pp 39ndash57 Kluwer Academic Publishers Dordrecht The Netherlands1994
[26] M Agarwal N Shrivastava andH Padh ldquoAdvances inmolecu-lar marker techniques and their applications in plant sciencesrdquoPlant Cell Reports vol 27 no 4 pp 617ndash631 2008
[27] S Preetha and T S Raveendren ldquoMolecular marker technologyin cottonrdquo Biotechnology and Molecular Biology Reviews vol 3no 2 pp 32ndash45 2008
[28] J R Andersen and T Lubberstedt ldquoFunctional markers inplantsrdquo Trends in Plant Science vol 8 no 11 pp 554ndash560 2003
[29] R K Kalia M K Rai S Kalia R Singh and A K DhawanldquoMicrosatellite markers an overview of the recent progress inplantsrdquo Euphytica vol 177 no 3 pp 309ndash334 2011
[30] N Appleby D Edwards and J Batley ldquoNew technologiesfor ultra-high throughput genotyping in plantsrdquo Methods inMolecular Biology vol 513 pp 19ndash39 2009
[31] Q H Xu X L Zhang and Y C Nie ldquoGenetic diversityevaluation of cultivars (G hirsumtum L) from the Changjiangriver valley and Tellow river valley by RAPD markersrdquo ActaGenetica Sinica vol 28 no 7 pp 683ndash690 2001
[32] H J Lu and G O Myers ldquoGenetic relationships and discrim-ination of ten influential upland cotton varieties using RAPDmarkersrdquoTheoretical and Applied Genetics vol 105 no 2-3 pp325ndash331 2002
[33] I Alvarez and J F Wendel ldquoCryptic interspecific introgressionand genetic differentiation within Gossypium aridum (Mal-vaceae) and its relativesrdquo Evolution vol 60 no 3 pp 505ndash5172006
[34] S Liu RGCantrell J CMcCarty Jr and JM Stewart ldquoSimplesequence repeat-based assessment of genetic diversity in cottonrace stock accessionsrdquoCrop Science vol 40 no 5 pp 1459ndash14692000
[35] L F Zhu X L Zhang and Y C Nie ldquoAnalysis of geneticdiversity in upland cotton (Gossypium hirsutum L) cultivarsfrom China and foreign countries by RAPDs and SSRsrdquo Journalof Agricultural Biotechnology vol 11 pp 450ndash455 2003
[36] M P Reddy N Sarla and E A Siddiq ldquoInter simple sequencerepeat (ISSR) polymorphism and its application in plant breed-ingrdquo Euphytica vol 128 no 1 pp 9ndash17 2002
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[39] Z H Yu Y H Park G R Lazo and R J KohelMolecularMap-ping of the Cotton Genome Agron Abstracts ASA MadisonWis USA 1997
[40] C L Brubaker A H Paterson and J F Wendel ldquoComparativegenetic mapping of allotetraploid cotton and its diploid progen-itorsrdquo Genome vol 42 no 2 pp 184ndash203 1999
[41] M Ulloa and W R Meredith Jr ldquoGenetic linkage map andQTL analysis of agronomic and fiber traits in an intraspecificpopulationrdquo Journal of Cotton Science vol 4 no 3 pp 161ndash1702000
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23populations and
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[43] A J Reinisch J-M Dong C L Brubaker D M Stelly J FWendel and A H Paterson ldquoA detailed RFLP map of cottonGossypium hirsutum x Gossypium barbadense chromosomeorganization and evolution in a disomic polyploid genomerdquoGenetics vol 138 no 3 pp 829ndash847 1994
[44] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoD-subgenome bias of Xcm resistance genes in tetraploidGossypium (cotton) suggests that polyploid formation hascreated novel avenues for evolutionrdquo Genetics vol 149 no 4pp 1987ndash1996 1998
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[47] S Khanam A Sham J L Bennetzen and M A M Aly ldquoAnal-ysis of molecular marker-based characterization and geneticvariation in date palm (Phoenix Dactylifera L)rdquo AustralianJournal of Crop Science vol 6 no 8 pp 1236ndash1244 2012
[48] K J Chalmers R Waugh J I Sprent A J Simons and WPowell ldquoDetection of genetic variation between and withinpopulations of Gliricidia sepium and G maculata using RAPDmarkersrdquo Heredity vol 69 pp 465ndash472 1992
[49] D S Multani and B R Lyon ldquoGenetic fingerprinting ofAustralian cotton cultivars with RAPD markersrdquo Genome vol38 no 5 pp 1005ndash1008 1995
[50] M KWajahatullah and J M Stewart ldquoGenomic affinity amongGossypium subgenus Sturtia species by RAPD analysisrdquo inProceeding of the Beltwide Cotton Conference National CottonCouncil p 452 Memphis Tenn USA 1997
[51] C D Geng Z Z Gong J Q Huang and Z C ZhangldquoIdentification of difference between cotton cultivars (G hirsu-tum) using the RAPD methodrdquo Jiangsu Journal of AgriculturalSciences vol 11 no 4 pp 21ndash24 1995
[52] T H Lan C G Cook and A H Paterson ldquoIdentification of aRAPDmarker linked tomale fertility restoration gene in cotton(Gossypium hirsutum L)rdquo Journal of Agricultural Genomics vol1 pp 1ndash5 1999
[53] B Shu K Fenling Z Y Yao Z G Mei Z Q Yuan and W XGang ldquoGenetic diversity analysis of representative elite cottonvarieties in three main cotton regions in China by RAPD andits relation with agronomic characteristicsrdquo Scientia AgriculturaSinica vol 34 pp 597ndash603 2001
[54] M Ulloa R G Cantrell R G Percy E Zeiger and Z Lu ldquoQTLanalysis of stomatal conductance and relationship to lint yieldin an interspecific cottonrdquo Journal of Cotton Science vol 4 no1 pp 10ndash18 2000
[55] B Bornet and M Branchard ldquoNonanchored inter simplesequence repeat (ISSR)markers reproducible and specific toolsfor genome fingerprintingrdquo Plant Molecular Biology Reportervol 19 no 3 pp 209ndash215 2001
[56] T M Culley and A D Wolfe ldquoPopulation genetic structureof the cleistogamous plant species Viola pubescens Aiton (Vio-laceae) as indicated by allozyme and ISSR molecular markersrdquoHeredity vol 86 no 5 pp 545ndash556 2000
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[58] T Nagaoka and Y Ogihara ldquoApplicability of inter-simplesequence repeat polymorphisms inwheat for use asDNAmark-ers in comparison to RFLP and RAPDmarkersrdquoTheoretical andApplied Genetics vol 94 no 5 pp 597ndash602 1997
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[60] A Shi S Kantartzi M Mmbaga and P Chen ldquoDevelopmentof ISSR PCR markers for diversity study in dogwood (Cornusspp)rdquo Agriculture and Biology Journal of North America vol 1pp 189ndash194 2010
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[62] B Bornet C Muller F Paulus and M Branchard ldquoHighlyinformative nature of inter simple sequence repeat (ISSR)sequences amplified using tri- and tetra-nucleotide primersfrom DNA of cauliflower (Brassica oleracea var botrytis L)rdquoGenome vol 45 no 5 pp 890ndash896 2002
[63] M Sica G Gamba S Montieri L Gaudio and S AcetoldquoISSR markers show differentiation among Italian populationsofAsparagus acutifolius Lrdquo BMCGenetics vol 6 article 17 2005
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[66] K Lukonge L Hersalman and M T Labuschagne ldquoGeneticdiversity of tanzanian cotton revealed by AFLP analysisrdquo inProceedings of the African Crop Science Conference vol 8 pp773ndash776 2007
[67] N Murtaza ldquoCotton genetic diversity study by AFLP markersrdquoElectronic Journal of Biotechnology vol 9 no 4 pp 456ndash4602006
[68] M Zhong J CMcCarty J N Jenkins and S Saha ldquoAssessmentof day-neutral backcross populations of cotton using AFLPmarkersrdquo Journal of Cotton Science vol 6 no 2 pp 97ndash1032002
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[70] A Badigannavar and G Myers ldquoGenetic analysis of AFLPmarkers associated with seed quality traits in upland cotton(Gossypium hirsutum)rdquo in Beltwide Cotton Conferences NewOrleans La USA 2010
[71] M K Altaf J M C D Stewart M K Wajahatullah J Zhangand R G Cantrell ldquoMolecular and morphological geneticsof a trispecies F2 population of cottonrdquo in Proceedings of theBeltwide Cotton Conferences vol 1 pp 448ndash452 New OrleansLa USA January 1997
[72] M K Rana and K V Bhat ldquoA comparison of AFLP andRAPD markers for genetic diversity and cultivar identificationin cottonrdquo Journal of Plant Biochemistry and Biotechnology vol13 no 1 pp 19ndash24 2004
[73] J-M Lacape T-B Nguyen S Thibivilliers et al ldquoA combinedRFLP-SSR-AFLP map of tetraploid cotton based on a Gossyp-ium hirsutum times Gossypium barbadense backcross populationrdquoGenome vol 46 no 4 pp 612ndash626 2003
[74] D TautzM Trick andG A Dover ldquoCryptic simplicity in DNAis amajor source of genetic variationrdquoNature vol 322 no 6080pp 652ndash656 1986
[75] S Saha J Wu J N Jenkins et al ldquoBreeding and genetics effectof chromosome substitutions from Gossypium barbadense L 3-79 into G hirsutum L TM-1 on agronomic and fiber traitsrdquoJournal of Cotton Science vol 8 no 3 pp 162ndash169 2004
[76] O U K Reddy A E Pepper I Abdurakhmonov et al ldquoNewdinucleotide and trinucleotide microsatellite marker resourcesfor cotton genome researchrdquo Journal of Cotton Science vol 5no 2 pp 103ndash113 2001
[77] T B Nguyen M Giband P Brottier A M Risterucci and JM Lascape ldquoWide coverage of the tetraploid cotton genomeusing newly developed microsatellite markersrdquoTheoretical andApplied Genetics vol 109 no 1 pp 167ndash175 2004
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[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
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Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
10 The Scientific World Journal
[12] Z J Chen B E Scheffler E Dennis et al ldquoToward sequencingcotton (Gossypium) genomesrdquo Plant Physiology vol 145 no 4pp 1303ndash1310 2007
[13] M J Iqbal O U K Reddy K M El-Zik and A E PepperldquoA genetic bottleneck in the lsquoevolution under domesticationrsquoof upland cotton Gossypium hirsutum L examined using DNAfingerprintingrdquoTheoretical and Applied Genetics vol 103 no 4pp 547ndash554 2001
[14] J O Beasley ldquoThe origin of American tetraploid GossypiumspeciesrdquoThe American Naturalist vol 74 pp 285ndash286 1940
[15] J O Beasley ldquoMeiotic chromosome behavior in species specieshybrids haploids and induced polyploids ofGossypiumrdquoGenet-ics vol 27 no 1 pp 25ndash54 1942
[16] J F Wendel C L Brubaker and A E Percival ldquoGeneticdiversity in Gossypium hirsutum and the origin of uplandcottonrdquoAmerican Journal of Botany vol 79 no 11 pp 1291ndash13101992
[17] A M Abdalla O U K Reddy K M El-Zik and A E PepperldquoGenetic diversity and relationships of diploid and tetraploidcottons revealed using AFLPrdquoTheoretical and Applied Geneticsvol 102 no 2-3 pp 222ndash229 2001
[18] X L Song X Z Sun T Z Zhang and H G Wang ldquoAdvanceson genetic diversity of cotton (Gossypium)rdquo Acta BotanicaBoreali-Occidentalia Sinica vol 24 pp 2393ndash2397 2004
[19] Z-S Zhang Y-H XiaoM Luo et al ldquoConstruction of a geneticlinkage map and QTL analysis of fiber-related traits in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 144 no 1-2 pp91ndash99 2005
[20] H-B Zhang Y Li BWang andPWChee ldquoRecent advances incotton genomicsrdquo International Journal of Plant Genomics vol2008 Article ID 742304 20 pages 2008
[21] K Arumuganathan and E D Earle ldquoNuclear DNA contentof some important plant speciesrdquo Plant Molecular BiologyReporter vol 9 no 3 pp 208ndash218 1991
[22] A H Paterson and R H Smith ldquoFuture horizons biotech-nology of cotton improvementrdquo in Cotton Origin HistoryTechnology and Production pp 415ndash432 John Wiley amp SonsNew York NY USA 1999
[23] V Tatineni R G Cantrell and D D Davis ldquoGenetic diversityin elite cotton germplasm determined by morphological char-acteristics and RAPDsrdquo Crop Science vol 36 no 1 pp 186ndash1921996
[24] C L Brubaker and J F Wendel ldquoRFLP diversity in cottonrdquo inGenetic Improvement of Cotton Emerging Technologies pp 81ndash101 Science Publishers Enfield NH USA 2001
[25] N D Young ldquoConstructing a plant genetic linkage map withDNA markersrdquo in DNA-Based Markers in Plants pp 39ndash57 Kluwer Academic Publishers Dordrecht The Netherlands1994
[26] M Agarwal N Shrivastava andH Padh ldquoAdvances inmolecu-lar marker techniques and their applications in plant sciencesrdquoPlant Cell Reports vol 27 no 4 pp 617ndash631 2008
[27] S Preetha and T S Raveendren ldquoMolecular marker technologyin cottonrdquo Biotechnology and Molecular Biology Reviews vol 3no 2 pp 32ndash45 2008
[28] J R Andersen and T Lubberstedt ldquoFunctional markers inplantsrdquo Trends in Plant Science vol 8 no 11 pp 554ndash560 2003
[29] R K Kalia M K Rai S Kalia R Singh and A K DhawanldquoMicrosatellite markers an overview of the recent progress inplantsrdquo Euphytica vol 177 no 3 pp 309ndash334 2011
[30] N Appleby D Edwards and J Batley ldquoNew technologiesfor ultra-high throughput genotyping in plantsrdquo Methods inMolecular Biology vol 513 pp 19ndash39 2009
[31] Q H Xu X L Zhang and Y C Nie ldquoGenetic diversityevaluation of cultivars (G hirsumtum L) from the Changjiangriver valley and Tellow river valley by RAPD markersrdquo ActaGenetica Sinica vol 28 no 7 pp 683ndash690 2001
[32] H J Lu and G O Myers ldquoGenetic relationships and discrim-ination of ten influential upland cotton varieties using RAPDmarkersrdquoTheoretical and Applied Genetics vol 105 no 2-3 pp325ndash331 2002
[33] I Alvarez and J F Wendel ldquoCryptic interspecific introgressionand genetic differentiation within Gossypium aridum (Mal-vaceae) and its relativesrdquo Evolution vol 60 no 3 pp 505ndash5172006
[34] S Liu RGCantrell J CMcCarty Jr and JM Stewart ldquoSimplesequence repeat-based assessment of genetic diversity in cottonrace stock accessionsrdquoCrop Science vol 40 no 5 pp 1459ndash14692000
[35] L F Zhu X L Zhang and Y C Nie ldquoAnalysis of geneticdiversity in upland cotton (Gossypium hirsutum L) cultivarsfrom China and foreign countries by RAPDs and SSRsrdquo Journalof Agricultural Biotechnology vol 11 pp 450ndash455 2003
[36] M P Reddy N Sarla and E A Siddiq ldquoInter simple sequencerepeat (ISSR) polymorphism and its application in plant breed-ingrdquo Euphytica vol 128 no 1 pp 9ndash17 2002
[37] C Schlotterer ldquoThe evolution of molecular markersmdashjust amatter of fashionrdquo Nature Reviews Genetics vol 5 no 1 pp63ndash69 2004
[38] C L Brubaker and J F Wendel ldquoReevaluating the origin ofdomesticated cotton (Gossypium hirsutum Malvaceae) usingnuclear restriction fragment length polymorphisms (RFLPs)rdquoAmerican Journal of Botany vol 81 no 10 pp 1309ndash1326 1994
[39] Z H Yu Y H Park G R Lazo and R J KohelMolecularMap-ping of the Cotton Genome Agron Abstracts ASA MadisonWis USA 1997
[40] C L Brubaker A H Paterson and J F Wendel ldquoComparativegenetic mapping of allotetraploid cotton and its diploid progen-itorsrdquo Genome vol 42 no 2 pp 184ndash203 1999
[41] M Ulloa and W R Meredith Jr ldquoGenetic linkage map andQTL analysis of agronomic and fiber traits in an intraspecificpopulationrdquo Journal of Cotton Science vol 4 no 3 pp 161ndash1702000
[42] M Ulloa W R Meredith Jr Z W Shappley and A L KahlerldquoRFLP genetic linkage maps from four F
23populations and
a joinmap of Gossypium hirsutum Lrdquo Theoretical and AppliedGenetics vol 104 no 2-3 pp 200ndash208 2002
[43] A J Reinisch J-M Dong C L Brubaker D M Stelly J FWendel and A H Paterson ldquoA detailed RFLP map of cottonGossypium hirsutum x Gossypium barbadense chromosomeorganization and evolution in a disomic polyploid genomerdquoGenetics vol 138 no 3 pp 829ndash847 1994
[44] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoD-subgenome bias of Xcm resistance genes in tetraploidGossypium (cotton) suggests that polyploid formation hascreated novel avenues for evolutionrdquo Genetics vol 149 no 4pp 1987ndash1996 1998
[45] H A Erlich PCR Technology Principles and Applications forDNA Amplification W H Freeman New York NY USA 1991
[46] J G KWilliams A R Kubelik K J Livak J A Rafalski and SV Tingey ldquoDNApolymorphisms amplified by arbitrary primers
The Scientific World Journal 11
are useful as geneticmarkersrdquoNucleic Acids Research vol 18 no22 pp 6531ndash6535 1990
[47] S Khanam A Sham J L Bennetzen and M A M Aly ldquoAnal-ysis of molecular marker-based characterization and geneticvariation in date palm (Phoenix Dactylifera L)rdquo AustralianJournal of Crop Science vol 6 no 8 pp 1236ndash1244 2012
[48] K J Chalmers R Waugh J I Sprent A J Simons and WPowell ldquoDetection of genetic variation between and withinpopulations of Gliricidia sepium and G maculata using RAPDmarkersrdquo Heredity vol 69 pp 465ndash472 1992
[49] D S Multani and B R Lyon ldquoGenetic fingerprinting ofAustralian cotton cultivars with RAPD markersrdquo Genome vol38 no 5 pp 1005ndash1008 1995
[50] M KWajahatullah and J M Stewart ldquoGenomic affinity amongGossypium subgenus Sturtia species by RAPD analysisrdquo inProceeding of the Beltwide Cotton Conference National CottonCouncil p 452 Memphis Tenn USA 1997
[51] C D Geng Z Z Gong J Q Huang and Z C ZhangldquoIdentification of difference between cotton cultivars (G hirsu-tum) using the RAPD methodrdquo Jiangsu Journal of AgriculturalSciences vol 11 no 4 pp 21ndash24 1995
[52] T H Lan C G Cook and A H Paterson ldquoIdentification of aRAPDmarker linked tomale fertility restoration gene in cotton(Gossypium hirsutum L)rdquo Journal of Agricultural Genomics vol1 pp 1ndash5 1999
[53] B Shu K Fenling Z Y Yao Z G Mei Z Q Yuan and W XGang ldquoGenetic diversity analysis of representative elite cottonvarieties in three main cotton regions in China by RAPD andits relation with agronomic characteristicsrdquo Scientia AgriculturaSinica vol 34 pp 597ndash603 2001
[54] M Ulloa R G Cantrell R G Percy E Zeiger and Z Lu ldquoQTLanalysis of stomatal conductance and relationship to lint yieldin an interspecific cottonrdquo Journal of Cotton Science vol 4 no1 pp 10ndash18 2000
[55] B Bornet and M Branchard ldquoNonanchored inter simplesequence repeat (ISSR)markers reproducible and specific toolsfor genome fingerprintingrdquo Plant Molecular Biology Reportervol 19 no 3 pp 209ndash215 2001
[56] T M Culley and A D Wolfe ldquoPopulation genetic structureof the cleistogamous plant species Viola pubescens Aiton (Vio-laceae) as indicated by allozyme and ISSR molecular markersrdquoHeredity vol 86 no 5 pp 545ndash556 2000
[57] J B Wang ldquoISSR markers and their applications in plantgeneticsrdquo Yi Chuan vol 24 no 5 pp 613ndash616 2002
[58] T Nagaoka and Y Ogihara ldquoApplicability of inter-simplesequence repeat polymorphisms inwheat for use asDNAmark-ers in comparison to RFLP and RAPDmarkersrdquoTheoretical andApplied Genetics vol 94 no 5 pp 597ndash602 1997
[59] M Z Galvan B Bornet P A Balatti and M BranchardldquoInter simple sequence repeat (ISSR) markers as a tool for theassessment of both genetic diversity and gene pool origin incommon bean (Phaseolus vulgaris L)rdquo Euphytica vol 132 no3 pp 297ndash301 2003
[60] A Shi S Kantartzi M Mmbaga and P Chen ldquoDevelopmentof ISSR PCR markers for diversity study in dogwood (Cornusspp)rdquo Agriculture and Biology Journal of North America vol 1pp 189ndash194 2010
[61] M W Blair O Panaud and S R McCouch ldquoInter-simplesequence repeat (ISSR) amplification for analysis of microsatel-litemotif frequency and fingerprinting in rice (Oryza sativa L)rdquoTheoretical and Applied Genetics vol 98 no 5 pp 780ndash7921999
[62] B Bornet C Muller F Paulus and M Branchard ldquoHighlyinformative nature of inter simple sequence repeat (ISSR)sequences amplified using tri- and tetra-nucleotide primersfrom DNA of cauliflower (Brassica oleracea var botrytis L)rdquoGenome vol 45 no 5 pp 890ndash896 2002
[63] M Sica G Gamba S Montieri L Gaudio and S AcetoldquoISSR markers show differentiation among Italian populationsofAsparagus acutifolius Lrdquo BMCGenetics vol 6 article 17 2005
[64] P Vos R Hogers M Bleeker et al ldquoAFLP a new technique forDNA fingerprintingrdquo Nucleic Acids Research vol 23 no 21 pp4407ndash4414 1995
[65] G O Myers B Jiang M W Akash A Badigannavar and SSaha ldquoChromosomal assignment of AFLP markers in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 165 no 2 pp391ndash399 2009
[66] K Lukonge L Hersalman and M T Labuschagne ldquoGeneticdiversity of tanzanian cotton revealed by AFLP analysisrdquo inProceedings of the African Crop Science Conference vol 8 pp773ndash776 2007
[67] N Murtaza ldquoCotton genetic diversity study by AFLP markersrdquoElectronic Journal of Biotechnology vol 9 no 4 pp 456ndash4602006
[68] M Zhong J CMcCarty J N Jenkins and S Saha ldquoAssessmentof day-neutral backcross populations of cotton using AFLPmarkersrdquo Journal of Cotton Science vol 6 no 2 pp 97ndash1032002
[69] A Rakshit S Rakshit J Singh et al ldquoAssociation of AFLPand SSR markers with agronomic and fibre quality traits inGossypium hirsutum Lrdquo Journal of Genetics vol 89 no 2 pp155ndash162 2010
[70] A Badigannavar and G Myers ldquoGenetic analysis of AFLPmarkers associated with seed quality traits in upland cotton(Gossypium hirsutum)rdquo in Beltwide Cotton Conferences NewOrleans La USA 2010
[71] M K Altaf J M C D Stewart M K Wajahatullah J Zhangand R G Cantrell ldquoMolecular and morphological geneticsof a trispecies F2 population of cottonrdquo in Proceedings of theBeltwide Cotton Conferences vol 1 pp 448ndash452 New OrleansLa USA January 1997
[72] M K Rana and K V Bhat ldquoA comparison of AFLP andRAPD markers for genetic diversity and cultivar identificationin cottonrdquo Journal of Plant Biochemistry and Biotechnology vol13 no 1 pp 19ndash24 2004
[73] J-M Lacape T-B Nguyen S Thibivilliers et al ldquoA combinedRFLP-SSR-AFLP map of tetraploid cotton based on a Gossyp-ium hirsutum times Gossypium barbadense backcross populationrdquoGenome vol 46 no 4 pp 612ndash626 2003
[74] D TautzM Trick andG A Dover ldquoCryptic simplicity in DNAis amajor source of genetic variationrdquoNature vol 322 no 6080pp 652ndash656 1986
[75] S Saha J Wu J N Jenkins et al ldquoBreeding and genetics effectof chromosome substitutions from Gossypium barbadense L 3-79 into G hirsutum L TM-1 on agronomic and fiber traitsrdquoJournal of Cotton Science vol 8 no 3 pp 162ndash169 2004
[76] O U K Reddy A E Pepper I Abdurakhmonov et al ldquoNewdinucleotide and trinucleotide microsatellite marker resourcesfor cotton genome researchrdquo Journal of Cotton Science vol 5no 2 pp 103ndash113 2001
[77] T B Nguyen M Giband P Brottier A M Risterucci and JM Lascape ldquoWide coverage of the tetraploid cotton genomeusing newly developed microsatellite markersrdquoTheoretical andApplied Genetics vol 109 no 1 pp 167ndash175 2004
12 The Scientific World Journal
[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
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International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
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BioinformaticsAdvances in
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Signal TransductionJournal of
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BioMed Research International
Evolutionary BiologyInternational Journal of
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Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Genetics Research International
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Enzyme Research
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International Journal of
Microbiology
The Scientific World Journal 11
are useful as geneticmarkersrdquoNucleic Acids Research vol 18 no22 pp 6531ndash6535 1990
[47] S Khanam A Sham J L Bennetzen and M A M Aly ldquoAnal-ysis of molecular marker-based characterization and geneticvariation in date palm (Phoenix Dactylifera L)rdquo AustralianJournal of Crop Science vol 6 no 8 pp 1236ndash1244 2012
[48] K J Chalmers R Waugh J I Sprent A J Simons and WPowell ldquoDetection of genetic variation between and withinpopulations of Gliricidia sepium and G maculata using RAPDmarkersrdquo Heredity vol 69 pp 465ndash472 1992
[49] D S Multani and B R Lyon ldquoGenetic fingerprinting ofAustralian cotton cultivars with RAPD markersrdquo Genome vol38 no 5 pp 1005ndash1008 1995
[50] M KWajahatullah and J M Stewart ldquoGenomic affinity amongGossypium subgenus Sturtia species by RAPD analysisrdquo inProceeding of the Beltwide Cotton Conference National CottonCouncil p 452 Memphis Tenn USA 1997
[51] C D Geng Z Z Gong J Q Huang and Z C ZhangldquoIdentification of difference between cotton cultivars (G hirsu-tum) using the RAPD methodrdquo Jiangsu Journal of AgriculturalSciences vol 11 no 4 pp 21ndash24 1995
[52] T H Lan C G Cook and A H Paterson ldquoIdentification of aRAPDmarker linked tomale fertility restoration gene in cotton(Gossypium hirsutum L)rdquo Journal of Agricultural Genomics vol1 pp 1ndash5 1999
[53] B Shu K Fenling Z Y Yao Z G Mei Z Q Yuan and W XGang ldquoGenetic diversity analysis of representative elite cottonvarieties in three main cotton regions in China by RAPD andits relation with agronomic characteristicsrdquo Scientia AgriculturaSinica vol 34 pp 597ndash603 2001
[54] M Ulloa R G Cantrell R G Percy E Zeiger and Z Lu ldquoQTLanalysis of stomatal conductance and relationship to lint yieldin an interspecific cottonrdquo Journal of Cotton Science vol 4 no1 pp 10ndash18 2000
[55] B Bornet and M Branchard ldquoNonanchored inter simplesequence repeat (ISSR)markers reproducible and specific toolsfor genome fingerprintingrdquo Plant Molecular Biology Reportervol 19 no 3 pp 209ndash215 2001
[56] T M Culley and A D Wolfe ldquoPopulation genetic structureof the cleistogamous plant species Viola pubescens Aiton (Vio-laceae) as indicated by allozyme and ISSR molecular markersrdquoHeredity vol 86 no 5 pp 545ndash556 2000
[57] J B Wang ldquoISSR markers and their applications in plantgeneticsrdquo Yi Chuan vol 24 no 5 pp 613ndash616 2002
[58] T Nagaoka and Y Ogihara ldquoApplicability of inter-simplesequence repeat polymorphisms inwheat for use asDNAmark-ers in comparison to RFLP and RAPDmarkersrdquoTheoretical andApplied Genetics vol 94 no 5 pp 597ndash602 1997
[59] M Z Galvan B Bornet P A Balatti and M BranchardldquoInter simple sequence repeat (ISSR) markers as a tool for theassessment of both genetic diversity and gene pool origin incommon bean (Phaseolus vulgaris L)rdquo Euphytica vol 132 no3 pp 297ndash301 2003
[60] A Shi S Kantartzi M Mmbaga and P Chen ldquoDevelopmentof ISSR PCR markers for diversity study in dogwood (Cornusspp)rdquo Agriculture and Biology Journal of North America vol 1pp 189ndash194 2010
[61] M W Blair O Panaud and S R McCouch ldquoInter-simplesequence repeat (ISSR) amplification for analysis of microsatel-litemotif frequency and fingerprinting in rice (Oryza sativa L)rdquoTheoretical and Applied Genetics vol 98 no 5 pp 780ndash7921999
[62] B Bornet C Muller F Paulus and M Branchard ldquoHighlyinformative nature of inter simple sequence repeat (ISSR)sequences amplified using tri- and tetra-nucleotide primersfrom DNA of cauliflower (Brassica oleracea var botrytis L)rdquoGenome vol 45 no 5 pp 890ndash896 2002
[63] M Sica G Gamba S Montieri L Gaudio and S AcetoldquoISSR markers show differentiation among Italian populationsofAsparagus acutifolius Lrdquo BMCGenetics vol 6 article 17 2005
[64] P Vos R Hogers M Bleeker et al ldquoAFLP a new technique forDNA fingerprintingrdquo Nucleic Acids Research vol 23 no 21 pp4407ndash4414 1995
[65] G O Myers B Jiang M W Akash A Badigannavar and SSaha ldquoChromosomal assignment of AFLP markers in uplandcotton (Gossypium hirsutum L)rdquo Euphytica vol 165 no 2 pp391ndash399 2009
[66] K Lukonge L Hersalman and M T Labuschagne ldquoGeneticdiversity of tanzanian cotton revealed by AFLP analysisrdquo inProceedings of the African Crop Science Conference vol 8 pp773ndash776 2007
[67] N Murtaza ldquoCotton genetic diversity study by AFLP markersrdquoElectronic Journal of Biotechnology vol 9 no 4 pp 456ndash4602006
[68] M Zhong J CMcCarty J N Jenkins and S Saha ldquoAssessmentof day-neutral backcross populations of cotton using AFLPmarkersrdquo Journal of Cotton Science vol 6 no 2 pp 97ndash1032002
[69] A Rakshit S Rakshit J Singh et al ldquoAssociation of AFLPand SSR markers with agronomic and fibre quality traits inGossypium hirsutum Lrdquo Journal of Genetics vol 89 no 2 pp155ndash162 2010
[70] A Badigannavar and G Myers ldquoGenetic analysis of AFLPmarkers associated with seed quality traits in upland cotton(Gossypium hirsutum)rdquo in Beltwide Cotton Conferences NewOrleans La USA 2010
[71] M K Altaf J M C D Stewart M K Wajahatullah J Zhangand R G Cantrell ldquoMolecular and morphological geneticsof a trispecies F2 population of cottonrdquo in Proceedings of theBeltwide Cotton Conferences vol 1 pp 448ndash452 New OrleansLa USA January 1997
[72] M K Rana and K V Bhat ldquoA comparison of AFLP andRAPD markers for genetic diversity and cultivar identificationin cottonrdquo Journal of Plant Biochemistry and Biotechnology vol13 no 1 pp 19ndash24 2004
[73] J-M Lacape T-B Nguyen S Thibivilliers et al ldquoA combinedRFLP-SSR-AFLP map of tetraploid cotton based on a Gossyp-ium hirsutum times Gossypium barbadense backcross populationrdquoGenome vol 46 no 4 pp 612ndash626 2003
[74] D TautzM Trick andG A Dover ldquoCryptic simplicity in DNAis amajor source of genetic variationrdquoNature vol 322 no 6080pp 652ndash656 1986
[75] S Saha J Wu J N Jenkins et al ldquoBreeding and genetics effectof chromosome substitutions from Gossypium barbadense L 3-79 into G hirsutum L TM-1 on agronomic and fiber traitsrdquoJournal of Cotton Science vol 8 no 3 pp 162ndash169 2004
[76] O U K Reddy A E Pepper I Abdurakhmonov et al ldquoNewdinucleotide and trinucleotide microsatellite marker resourcesfor cotton genome researchrdquo Journal of Cotton Science vol 5no 2 pp 103ndash113 2001
[77] T B Nguyen M Giband P Brottier A M Risterucci and JM Lascape ldquoWide coverage of the tetraploid cotton genomeusing newly developed microsatellite markersrdquoTheoretical andApplied Genetics vol 109 no 1 pp 167ndash175 2004
12 The Scientific World Journal
[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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International Journal of
Volume 2014
Zoology
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ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Enzyme Research
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International Journal of
Microbiology
12 The Scientific World Journal
[78] R K Varshney A Graner and M E Sorrells ldquoGenicmicrosatellite markers in plants features and applicationsrdquoTrends in Biotechnology vol 23 no 1 pp 48ndash55 2005
[79] R V Kantety M La Rota D E Matthews and M E Sor-rells ldquoData mining for simple sequence repeats in expressedsequence tags from barley maize rice sorghum and wheatrdquoPlant Molecular Biology vol 48 no 5-6 pp 501ndash510 2002
[80] H-Y Zhu T-Z Zhang L-M Yang and W-Z Guo ldquoEST-SSRsequences revealed the relationship of D-genome in diploid andtetraploid Species in Gossypiumrdquo Plant Science vol 176 no 3pp 397ndash405 2009
[81] L F Gao R L Jing N X Huo et al ldquoOne hundred and onenew microsatellite loci derived from ESTs (EST-SSRs) in breadwheatrdquoTheoretical andAppliedGenetics vol 108 no 7 pp 1392ndash1400 2004
[82] P W Chee J Rong D Williams-Coplin S R Schulze and AH Paterson ldquoEST derived PCR-based markers for functionalgene homologues in cottonrdquo Genome vol 47 no 3 pp 449ndash462 2004
[83] Z-G Han W-Z Guo X-L Song and T-Z Zhang ldquoGeneticmapping of EST-derived microsatellites from the diploidGossypium arboreum in allotetraploid cottonrdquo MolecularGenetics and Genomics vol 272 no 3 pp 308ndash327 2004
[84] Z Han C Wang X Song et al ldquoCharacteristics developmentand mapping of Gossypium hirsutum derived EST-SSRs inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 112no 3 pp 430ndash439 2006
[85] J A Udall J M Swanson K Haller et al ldquoA global assembly ofcotton ESTsrdquoGenome Research vol 16 no 3 pp 441ndash450 2006
[86] A G Ince M Karaca and A N Onus ldquoCAPS-microsatellitesuse of CAPS method to convert non-polymorphic microsatel-lites into useful markersrdquoMolecular Breeding vol 25 no 3 pp491ndash499 2010
[87] K Semagn A Bjoslashrnstad and M N Ndjiondjop ldquoAn overviewof molecular marker methods for plantsrdquo African Journal ofBiotechnology vol 5 no 25 pp 2540ndash2568 2006
[88] AKonieczny andFMAusubel ldquoAprocedure formappingAra-bidopsis mutations using co-dominant ecotype-specific PCR-based markersrdquo Plant Journal vol 4 no 2 pp 403ndash410 1993
[89] M Karaca and A G Ince ldquoNew non-redundant microsatelliteand CAPS-microsatellite markers for cotton (Gossypium L)rdquoTurkish Journal of Field Crops vol 16 no 2 pp 172ndash178 2011
[90] K O Ayeh ldquoExpressed sequence tags (ESTs) and singlenucleotide polymorphisms (SNPs) emergingmolecularmarkertools for improving agronomic traits in plant biotechnologyrdquoAfrican Journal of Biotechnology vol 7 no 4 pp 331ndash341 2008
[91] I Richard and J S Beckmann ldquoHow neutral are synonymouscodon mutationsrdquo Nature genetics vol 10 no 3 article 2591995
[92] T Shaheen M Asif and Y Zafar ldquoSingle nucleotide polymor-phism analysis of MT-SHSP gene of Gossypium arboreum andits relationship with other diploid cotton genomes G hirsutumandArabidopsis thalianardquoPakistan Journal of Botany vol 41 no1 pp 177ndash183 2009
[93] R L Byers D B Harker S M Yourstone P J Maughanand J A Udall ldquoDevelopment and mapping of SNP assays inallotetraploid cottonrdquoTheoretical and Applied Genetics vol 124no 7 pp 1201ndash1214 2012
[94] W B Barbazuk S J Emrich H D Chen L Li and P SSchnable ldquoSNP discovery via 454 transcriptome sequencingrdquoPlant Journal vol 51 no 5 pp 910ndash918 2007
[95] C P van Tassell T P L Smith L K Matukumalli et al ldquoSNPdiscovery and allele frequency estimation by deep sequencingof reduced representation librariesrdquo Nature Methods vol 5 no3 pp 247ndash252 2008
[96] N A Baird P D Etter T S Atwood et al ldquoRapid SNP discoveryand genetic mapping using sequenced RAD markersrdquo PLoSONE vol 3 no 10 Article ID e3376 2008
[97] P C Bundock F G Eliott G Ablett et al ldquoTargeted singlenucleotide polymorphism (SNP) discovery in a highly poly-ploid plant species using 454 sequencingrdquo Plant BiotechnologyJournal vol 7 no 4 pp 347ndash354 2009
[98] C An S Saha J N Jenkins et al ldquoCotton (Gossypium spp)R2R3-MYB transcription factors SNP identification phyloge-nomic characterization chromosome localization and linkagemappingrdquo Theoretical and Applied Genetics vol 116 no 7 pp1015ndash1026 2008
[99] A van Deynze K Stoffel M Lee et al ldquoSampling nucleotidediversity in cottonrdquo BMC Plant Biology vol 9 article 125 2009
[100] R R Mir P J Hiremath O Riera-Lizarazu and R K VarshneyldquoEvolvingmolecularmarker technologies in plants fromRFLPsto GBSrdquo in Diagnostics in Plant Breeding vol 11 pp 229ndash247Springer Amsterdam The Netherlands 2013
[101] R J Elshire J C Glaubitz Q Sun et al ldquoA robust simplegenotyping-by-sequencing (GBS) approach for high diversityspeciesrdquo PLoS ONE vol 6 no 5 Article ID e19379 2011
[102] J A Poland P J Brown M E Sorrells and J-L JanninkldquoDevelopment of high-density genetic maps for barley andwheat using a novel two-enzyme genotyping-by-sequencingapproachrdquo PLoS ONE vol 7 no 2 Article ID e32253 2012
[103] X Huang X Wei T Sang et al ldquoGenome-wide asociationstudies of 14 agronomic traits in rice landracesrdquoNatureGeneticsvol 42 no 11 pp 961ndash967 2010
[104] A A Dahab M Saeed B B Mohamed et al ldquoGenetic diversityassessment of cotton (Gossypium hirsutum L) genotypes fromPakistan using simple sequence repeat markerrdquo AustralianJournal of Crop Science vol 7 no 2 pp 261ndash267 2013
[105] J R Russell J D Fuller M Macaulay et al ldquoDirect comparisonof levels of genetic variation among barley accessions detectedby RFLPs AFLPs SSRs and RAPDsrdquo Theoretical and AppliedGenetics vol 95 no 4 pp 714ndash722 1997
[106] M Pillay and G O Myers ldquoGenetic diversity in cotton assessedby variation in ribosomal RNA genes and AFLP markersrdquo CropScience vol 39 no 6 pp 1881ndash1886 1999
[107] I Ullah A Iram M Z Iqbal M Nawaz S M Hasni andS Jamil ldquoGenetic diversity analysis of Bt cotton genotypes inPakistan using simple sequence repeat markersrdquo Genetics andMolecular Research vol 11 no 1 pp 597ndash605 2012
[108] M Vafaie-Tabar S Chandrashekaran R P Singh and M KRana ldquoEvaluation of genetic diversity in Indian tetraploid anddiploid cotton (Gossypium spp) by morphological characteris-tics and RAPDsrdquo Indian Journal of Genetics and Plant Breedingvol 63 no 3 pp 230ndash234 2003
[109] S S Mehetre M Gomes E Susan A R Aher and G CShinde ldquoRAPD and cytomorphological analyses of F
1 F2
and amphidiploid (A1) generations of Gossypium arboreum times
Gossypium capitis-viridisrdquo Cytologia vol 69 no 4 pp 367ndash3792004
[110] M K Rana S Singh and K V Bhat ldquoRAPD STMS and ISSRmarkers for genetic diversity and hybrid seed purity testing incottonrdquo Seed Science and Technology vol 35 no 3 pp 709ndash7212007
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
The Scientific World Journal 13
[111] M Sheidai F Yahyazadeh F Farahanei and Z Noormoham-mad ldquoGenetic and morphological variations induced by tissueculture in tetraploid cotton (Gossypium hirsutum L)rdquo ActaBiologica Szegediensis vol 52 no 1 pp 33ndash38 2008
[112] M Sheidai L Bahrami A Majd Z Noormohammadi andO Alishah ldquoGenetic diversity in F2 back-cross progenies ofcottonrdquo Gene Conserve vol 9 pp 167ndash187 2010
[113] M J Iqbal N Aziz N A Saeed Y Zafar and K A MalikldquoGenetic diversity evaluation of some elite cotton varieties byRAPD analysisrdquoTheoretical and Applied Genetics vol 94 no 1pp 139ndash144 1997
[114] X Y Wang W Z Guo T Z Zhang and J J Pan ldquoAnalysisof RAPD fingerprinting on short-seasonal cotton cultivars inChinardquo Acta Agronomica Sinica vol 23 pp 669ndash676 1997
[115] S A Khan DHussain E Askari JM Stewart K AMalik andY Zafar ldquoMolecular phylogeny of Gossypium species by DNAfingerprintingrdquoTheoretical and Applied Genetics vol 101 no 5-6 pp 931ndash938 2000
[116] A S Mumtaz M Naveed and Z K Shinwari ldquoAssessmentof genetic diversity and germination pattern in selected cottongenotypes of Pakistanrdquo Pakistan Journal of Botany vol 42 no6 pp 3949ndash3956 2010
[117] I Vroh Bi A Maquet J P Baudoin P du Jardin J MJacquemin and G Mergeai ldquoBreeding for rsquolow-gossypol seedand high-gossypol plantsrsquo in upland cotton Analysis of tri-species hybrids and backcross progenies using AFLPs andmapped RFLPsrdquo Theoretical and Applied Genetics vol 99 no7-8 pp 1233ndash1244 1999
[118] S Saha M Karaca J N Jenkins A E Zipf O U K Reddy andR V Kantety ldquoSimple sequence repeats as useful resources tostudy transcribed genes of cottonrdquo Euphytica vol 130 no 3 pp355ndash364 2003
[119] S Liu S Saha D Stelly B Burr and R G Cantrell ldquoChro-mosomal assignment of microsatellite loci in cottonrdquo Journalof Heredity vol 91 no 4 pp 326ndash332 2000
[120] O A Gutierrez S Basu S Saha et al ldquoGenetic distanceamong selected cotton genotypes and its relationship with F2performancerdquo Crop Science vol 42 no 6 pp 1841ndash1847 2002
[121] D Rungis D Llewellyn E S Dennis and B R Lyon ldquoSimplesequence repeat (SSR) markers reveal low levels of poly-morphism between cotton (Gossypium hirsutum L) cultivarsrdquoAustralian Journal of Agricultural Research vol 56 no 3 pp301ndash307 2005
[122] J E Frelichowski Jr M B Palmer D Main et al ldquoCottongenomemapping with newmicrosatellites fromAcala ldquoMaxxardquoBAC-endsrdquoMolecularGenetics andGenomics vol 275 no 5 pp479ndash491 2006
[123] C H C de Magalhaes Bertini I Schuster T Sediyama E Gde Barros and M A Moreira ldquoCharacterization and geneticdiversity analysis of cotton cultivars using microsatellitesrdquoGenetics andMolecular Biology vol 29 no 2 pp 321ndash329 2006
[124] G Chen and X-M Du ldquoGenetic diversity of source germplasmof upland cotton in China as determined by SSR markeranalysisrdquo Acta Genetica Sinica vol 33 no 8 pp 733ndash745 2006
[125] X Q Wang C H Feng Z X Lin and X L Zhang ldquoGeneticdiversity of sea-island cotton (Gossypium barbadense) revealedby mapped SSRsrdquo Genetics and molecular research GMR vol10 no 4 pp 3620ndash3631 2011
[126] D D Fang L L Hinze R G Percy P Li D Deng andG Thyssen ldquoA microsatellite-based genome-wide analysis ofgenetic diversity and linkage disequilibrium in Upland cotton
(Gossypium hirsutum L) cultivars from major cotton-growingcountriesrdquo Euphytica vol 191 no 3 pp 391ndash401 2013
[127] P Selvakumar R Ravikesavan A Gopikrishnan KThiyagu SPreetha and N M Boopathi ldquoGenetic purity analysis of cotton(Gossypium spp) hybrids using SSR markersrdquo Seed Science andTechnology vol 38 no 2 pp 358ndash366 2010
[128] B C Y Collard M Z Z Jahufer J B Brouwer and E C KPang ldquoAn introduction tomarkers quantitative trait loci (QTL)mapping and marker-assisted selection for crop improvementthe basic conceptsrdquo Euphytica vol 142 no 1-2 pp 169ndash1962005
[129] A H Paterson ldquoMaking genetic mapsrdquo in Genome Mappingin Plants pp 23ndash39 RG Landes Company Austin Tex USAAcademic Press San Diego Calif USA 1996
[130] A H Paterson ldquoMapping genes responsible for differencesin phenotyperdquo in Genome Mapping in Plants pp 41ndash54 R GLandes San Diego Calif USA Academic Press Austin TexUSA 1996
[131] C-X Jiang R J Wright K M El-Zik and A H PatersonldquoPolyploid formation created unique avenues for response toselection in Gossypium (cotton)rdquo Proceedings of the NationalAcademy of Sciences of the United States of America vol 95 no8 pp 4419ndash4424 1998
[132] R J Wright P M Thaxton K M El-Zik and A H PatersonldquoMolecular mapping of genes affecting pubescence of cottonrdquoJournal of Heredity vol 90 no 1 pp 215ndash219 1999
[133] Y Saranga M Menz C-X Jiang R J Wright D Yakir and AH Paterson ldquoGenomic dissection of genotype x environmentinteractions conferring adaptation of cotton to arid conditionsrdquoGenome Research vol 11 no 12 pp 1988ndash1995 2001
[134] P W Chee X Draye C X Jiang et al ldquoMolecular dissectionof phenotypic variation between Gossypium hirsutum andGossypium barbadense (cotton) by a backcross-self approachIII Fiber lengthrdquo Theoretical and Applied Genetics vol 111 no4 pp 772ndash781 2005
[135] R J Kohel J Yu Y-H Park and G R Lazo ldquoMolecularmapping and characterization of traits controlling fiber qualityin cottonrdquo Euphytica vol 121 no 2 pp 163ndash172 2001
[136] X ShenW Guo X Zhu et al ldquoMolecular mapping of QTLs forfiber qualities in three diverse lines in Upland cotton using SSRmarkersrdquoMolecular Breeding vol 15 no 2 pp 169ndash181 2005
[137] B-H Wang Y-T Wu N-T Huang X-F Zhu W-Z Guoand T-Z Zhang ldquoQTL mapping for plant architecture traitsin upland cotton using RILs and SSR markersrdquo Acta GeneticaSinica vol 33 no 2 pp 161ndash170 2006
[138] H Qin W Guo Y-M Zhang and T Zhang ldquoQTL mappingof yield and fiber traits based on a four-way cross populationinGossypium hirsutum LrdquoTheoretical and Applied Genetics vol117 no 6 pp 883ndash894 2008
[139] J Z Yu R J Kohe D D Fang et al ldquoA high-density simplesequence repeat and single nucleotide polymorphism geneticmap of the tetraploid cotton genomerdquo G3 Genes GenomesGenetics vol 2 no 1 pp 43ndash58 2012
[140] C Li XWang N Dong et al ldquoQTL analysis for early-maturingtraits in cotton using two upland cotton (Gossypium hirsutumL) crossesrdquo Breeding Science vol 63 no 2 pp 154ndash163 2013
[141] M Mei N H Syed W Gao et al ldquoGenetic mapping andQTL analysis of fiber-related traits in cotton (Gossypium)rdquoTheoretical and Applied Genetics vol 108 no 2 pp 280ndash2912004
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
14 The Scientific World Journal
[142] M Nordborg and S Tavare ldquoLinkage disequilibrium whathistory has to tell usrdquoTrends inGenetics vol 18 no 2 pp 83ndash902002
[143] S Myles J Peiffer P J Brown et al ldquoAssociation mappingcritical considerations shift from genotyping to experimentaldesignrdquoThe Plant Cell vol 21 no 8 pp 2194ndash2202 2009
[144] C Zhu M Gore E S Buckler and J Yu ldquoStatus and prospectsof association mapping in plantsrdquoThe Plant Genome vol 1 no1 pp 5ndash20 2008
[145] I Y Abdurakhmonov ldquoExploiting genetic diversityrdquo in Proceed-ings of the World Cotton Research Conference vol 1 pp 10ndash14Lubbock Tex USA 2007
[146] A Barnaud T Lacombe and A Doligez ldquoLinkage disequilib-rium in cultivated grapevine Vitis vinifera Lrdquo Theoretical andApplied Genetics vol 112 no 4 pp 708ndash716 2006
[147] I Y Abdurakhmonov S Saha J N Jenkins et al ldquoLinkagedisequilibrium based association mapping of fiber quality traitsin G hirsutum L variety germplasmrdquo Genetica vol 136 no 3pp 401ndash417 2009
[148] D Edwards and J Batley ldquoPlant genome sequencing applica-tions for crop improvementrdquo Plant Biotechnology Journal vol8 no 1 pp 2ndash9 2010
[149] N F Weeden G M Timmerman and J Lu ldquoIdentifying andmapping genes of economic significancerdquo Euphytica vol 73 no1-2 pp 191ndash198 1993
[150] N D Young ldquoQTLmapping and quantitative disease resistancein plantsrdquo Annual Review of Phytopathology vol 34 pp 479ndash501 1996
[151] V H Coryell H Jessen J M Schupp D Webb and P KeimldquoAllele-specific hybridization markers for soybeanrdquo Theoreticaland Applied Genetics vol 98 no 5 pp 690ndash696 1999
[152] G Mergeai J P Baudoin and B I Vroh ldquoProduction of highgossypol cotton plants with low gossypol seed from trispecifichybrids including Gossypium sturtianumrdquo in proceedings of theWorld Cotton Research Conference vol 2 pp 206ndash210 AthensGreece september 1998
[153] T Zhang Y Yuan J Yu W Guo and R J Kohel ldquoMoleculartagging of a major QTL for fiber strength in upland cotton andits marker-assisted selectionrdquoTheoretical and Applied Geneticsvol 106 no 2 pp 262ndash268 2003
[154] W Guo T Zhang X Shen J Z Yu and R J Kohel ldquoDevel-opment of SCAR marker linked to a major QTL for high fiberstrength and its usage in molecular-marker assisted selection inupland cottonrdquoCrop Science vol 43 no 6 pp 2252ndash2256 2003
[155] D D Fang J Xiao P C Canci and R G Cantrell ldquoA new SNPhaplotype associated with blue disease resistance gene in cotton(Gossypium hirsutum L)rdquoTheoretical and Applied Genetics vol120 no 5 pp 943ndash953 2010
[156] G Sunilkumar L M Campbell L Puckhaber R D Stipanovicand K S Rathore ldquoEngineering cottonseed for use in humannutrition by tissue-specific reduction of toxic gossypolrdquo Pro-ceedings of the National Academy of Sciences of the United Statesof America vol 103 no 48 pp 18054ndash18059 2006
[157] B Hendrix and J M Stewart ldquoEstimation of the nuclear DNAcontent of Gossypium speciesrdquo Annals of Botany vol 95 no 5pp 789ndash797 2005
[158] L Lin G J Pierce J E Bowers et al ldquoA draft physical mapof a D-genome cotton species (Gossypium raimondii)rdquo BMCGenomics vol 11 no 1 article 395 2010
[159] K Wang Z Wang F Li et al ldquoThe draft genome of a diploidcotton Gossypium raimondiirdquo Nature Genetics vol 44 no 10pp 1098ndash1103 2012
[160] F Li G Fan KWang et al ldquoGenome sequence of the cultivatedcottonGossypium arboreumrdquoNature Genetics vol 46 no 6 pp567ndash572 2014
[161] P Chee E Lubbers O May J Gannaway and A H PatersonldquoChanges in genetic diversity of the US upland cottonrdquo inProceedings of the Beltwide Cotton Conference National CottonCouncil San Antonio Tex USA 2004
[162] E Lubbers P Chee J Gannaway R Wright K El-Zik and AH Paterson ldquoLevels and patterns of genetic diversity in uplandcottonrdquo in Proceedings of the Plant and Animal Genome 12thConference San Diego Calif USA 2004
[163] H-M Wang Z-X Lin X-L Zhang et al ldquoMapping andquantitative trait loci analysis of verticillium wilt resistancegenes in cottonrdquo Journal of Integrative Plant Biology vol 50 no2 pp 174ndash182 2008
[164] C Niu H E Lister B Nguyen T A Wheeler and R J WrightldquoResistance toThielaviopsis basicola in the cultivated a genomecottonrdquoTheoretical andApplied Genetics vol 117 no 8 pp 1313ndash1323 2008
[165] C Niu D J Hinchliffe R G Cantrell C Wang P A Robertsand J Zhang ldquoIdentification of molecular markers associatedwith root-knot nematode resistance in upland cottonrdquo CropScience vol 47 no 3 pp 951ndash960 2007
[166] V Korzun ldquoUse of molecular markers in cereal breedingrdquoCellular and Molecular Biology Letters vol 7 no 2 pp 811ndash8202002
[167] E Jones W-C Chu M Ayele et al ldquoDevelopment of singlenucleotide polymorphism (SNP)markers for use in commercialmaize (Zea mays L) germplasmrdquo Molecular Breeding vol 24no 2 pp 165ndash176 2009
[168] S Deschamps V Llaca and G D May ldquoGenotyping-by-sequencing in plantsrdquo Biology vol 1 no 3 pp 460ndash483 2012
[169] T Yasmin N Tabbasam I Ullah M Asif and Y ZafarldquoStudying the extent of genetic diversity among Gossypiumarboreum L genotypescultivars using DNA fingerprintingrdquoGenetic Resources and Crop Evolution vol 55 no 3 pp 331ndash3392008
[170] Z Noormohammadi M T S Al-Rubaye M Sheidai and OAlishah ldquoISSR RAPD and agronomic study in some F
1and F
2
cotton genotypesrdquo Acta Biologica Szegediensis vol 55 no 2 pp219ndash225 2011
[171] A B Dongre M P Raut V M Paikrao and S S PandeldquoGenetic purity testing of cotton F1 hybrid DHH-11 and parentsrevealed by molecular markersrdquo International Research Journalof Biotechnology vol 3 no 2 pp 32ndash36 2012
[172] Z Noormohammadi Y H-A Farahani M Sheidai S GBaraki and O Alishah ldquoGenetic diversity analysis in Opalcotton hybrids based on SSR ISSR and RAPD markersrdquoGenetics andMolecular Research vol 12 no 1 pp 256ndash269 2013
[173] J Zhang Y Lu R G Cantrell and EHughs ldquoMolecularmarkerdiversity and field performance in commercial cotton cultivarsevaluated in the southwestern USArdquo Crop Science vol 45 no4 pp 1483ndash1490 2005
[174] D Liu X Guo Z Lin Y Nie and X Zhang ldquoGenetic diversityof Asian cotton (Gossypium arboreum L) in China evaluated bymicrosatellite analysisrdquo Genetic Resources and Crop Evolutionvol 53 no 6 pp 1145ndash1152 2006
[175] W-Z Guo B-L Zhou L-M Yang W Wang and T-Z ZhangldquoGenetic diversity of landraces in Gossypium arboreum L Racesinense assessed with simple sequence repeat markersrdquo Journalof Integrative Plant Biology vol 48 no 9 pp 1008ndash1017 2006
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
The Scientific World Journal 15
[176] J-M Lacape D Dessauw M Rajab J-L Noyer and B HauldquoMicrosatellite diversity in tetraploid Gossypium germplasmassembling a highly informative genotyping set of cotton SSRsrdquoMolecular Breeding vol 19 no 1 pp 45ndash58 2007
[177] S K Kantartzi M Ulloa E Sacks and J M Stewart ldquoAssessinggenetic diversity in Gossypium arboreum L cultivars usinggenomic and EST-derived microsatellitesrdquo Genetica vol 136no 1 pp 141ndash147 2009
[178] A Qayyum N Murtaza F M Azhar andW Malik ldquoBiodiver-sity and nature of gene action for oil and protein contents inGossypium hirsutum L estimated by SSR markersrdquo Journal ofFood Agriculture and Environment vol 7 no 2 pp 590ndash5932009
[179] Y Zhang X F Wang Z K Li G Y Zhang and Z YMa ldquoAssessing genetic diversity of cotton cultivars usinggenomic and newly developed expressed sequence tag-derivedmicrosatellite markersrdquo Genetics and Molecular Research vol10 no 3 pp 1462ndash1470 2011
[180] A Kalivas F Xanthopoulos O Kehagia and A S TsaftarisldquoAgronomic characterization genetic diversity and associationanalysis of cotton cultivars using simple sequence repeatmolec-ularmarkersrdquoGenetics andMolecular Research vol 10 no 1 pp208ndash217 2011
[181] P Tyagi M A Gore D T Bowman B T Campbell J A Udalland V Kuraparthy ldquoGenetic diversity and population structurein the US Upland cotton (Gossypium hirsutum L)rdquo Theoreticaland Applied Genetics vol 127 pp 283ndash295 2013
[182] M K Rana V P Singh and K V Bhat ldquoAssessment of geneticdiversity in upland cotton (Gossypium hirsutum L) breedinglines by using amplified fragment length polymorphism (AFLP)markers and morphological characteristicsrdquo Genetic Resourcesand Crop Evolution vol 52 no 8 pp 989ndash997 2005
[183] O T Westengen Z Huaman and M Heun ldquoGenetic diversityand geographic pattern in early South American cotton domes-ticationrdquo Theoretical and Applied Genetics vol 110 no 2 pp392ndash402 2005
[184] S Ahmad T Zhang N Islam S Tayyaba and M RahmanldquoIdentifying genetic variation in Gossypium based on singlenucleotide polymorphismrdquo Pakistan Journal of Botany vol 39no 4 pp 1245ndash1250 2007
[185] X Draye P Chee C-X Jiang et al ldquoMolecular dissection ofinterspecific variation between Gossypium hirsutum and Gbarbadense (cotton) by a backcross-self approach II Fiberfinenessrdquo Theoretical and Applied Genetics vol 111 no 4 pp764ndash771 2005
[186] Z-S Zhang M-C Hu J Zhang et al ldquoConstruction ofa comprehensive PCR-based marker linkage map and QTLmapping for fiber quality traits in upland cotton (Gossypiumhirsutum L)rdquoMolecular Breeding vol 24 no 1 pp 49ndash61 2009
[187] B Wang W Guo X Zhu Y Wu N Huang and T ZhangldquoQTL mapping of fiber quality in an elite hybrid derived-RILpopulation of upland cottonrdquo Euphytica vol 152 no 3 pp 367ndash378 2006
[188] K Zhang J Zhang J Ma et al ldquoGenetic mapping and quantita-tive trait locus analysis of fiber quality traits using a three-parentcomposite population in upland cotton (Gossypium hirsutumL)rdquoMolecular Breeding vol 29 no 2 pp 335ndash348 2012
[189] J Wu O A Gutierrez J N Jenkins J C McCarty and J ZhuldquoQuantitative analysis and QTL mapping for agronomic andfiber traits in an RI population of upland cottonrdquo Euphytica vol165 no 2 pp 231ndash245 2009
[190] X ShenW Guo Q Lu X Zhu Y Yuan and T Zhang ldquoGeneticmapping of quantitative trait loci for fiber quality and yield traitby RIL approach in upland cottonrdquo Euphytica vol 155 no 3 pp371ndash380 2007
[191] R Liu B Wang W Guo et al ldquoQuantitative trait loci mappingfor yield and its components by using two immortalizedpopulations of a heterotic hybrid in Gossypium hirsutum LrdquoMolecular Breeding vol 29 no 2 pp 297ndash311 2012
[192] D H He Z X Lin X L Zhang et al ldquoQTL mapping foreconomic traits based on a dense genetic map of cotton withPCR-based markers using the interspecific cross of Gossypiumhirsutum x Gossypium barbadenserdquo Euphytica vol 153 no 1-2pp 181ndash197 2007
[193] C Jiang R J Wright S S Woo T A DelMonte and AH Paterson ldquoQTL analysis of leaf morphology in tetraploidGossypium (cotton)rdquoTheoretical and Applied Genetics vol 100no 3-4 pp 409ndash418 2000
[194] Y Guo J C McCarty J N Jenkins and S Saha ldquoQTLs fornode of first fruiting branch in a cross of an upland cottonGossypium hirsutum L cultivar with primitive accession Texas701rdquo Euphytica vol 163 no 1 pp 113ndash122 2008
[195] R M D Koebner and R W Summers ldquo21st century wheatbreeding plot selection or plate detectionrdquo Trends in Biotech-nology vol 21 no 2 pp 59ndash63 2003
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
![Review Article Strategies of Intracellular Pathogens for ...downloads.hindawi.com/journals/bmri/2015/476534.pdf · monocytogenes, Neisseria spp., and Shigella spp. [ , ]. Obligate](https://static.fdocumentos.tips/doc/165x107/5ec8c8515e733d5a8b77e115/review-article-strategies-of-intracellular-pathogens-for-monocytogenes-neisseria.jpg)
![ARTÍCULO DE REvisión / Review ARTiCLe · Segundo Li et al. [3], uma solução viável no gerenciamento do lixo nos países desenvolvidos e industrializados é a incineração de](https://static.fdocumentos.tips/doc/165x107/5be4f51309d3f28a428b67da/articulo-de-revision-review-segundo-li-et-al-3-uma-solucao-viavel.jpg)
