Genetic Analysis of Cotton Fiber Traits by Molecular Markers

1.Development of EST-SSRs derived from G.barbadense:One hundred and nineteen EST-SSRs were developed based on 98 unique ESTs from a cDNA library constructed in our laboratory using developing fibers from G.barbadense cv.3-79.Among the SSRs,trinucleotide AAG appeared

Genetic variability for yield and fiber related traits in genetically modified cotton

Background:Cotton(Gossypium hirsutum L.)is grown for fiber and oil purposes in tropical and sub-tropical areas of the world.Pakistan is the 4th largest producer of cotton.It has a significant contribution in the GDP of Pakistan.Therefore,the present study was performed to assess the genetic variations and genetic diversity of yield and fiber quality traits in cotton and to analyze the associations present among them.Results:Analysis of variance exhibited significant variation for all studied traits except total number of nodes and the height to node ratio.The phenotypic coefficient of variation was higher than the genotypic coefficient of variation for all studied traits.Plant height,monopodial branches,total number of bolls,lint index,seed index,and seed cotton yield displayed high heritabilities in a broad sense with maximum genetic advanee.Correlation analysis revealed that seed cotton yield had a significant positive association with plant height,the nu mber of monopodial branches,the nu mber of sympodia I branches,ginning outturn(GOT),the number of bolls,seed per boll,seed index,uniformity index,the number of sympodial branches,reflectance,and seed index at the genotypic level while a significant positive relationship was observed with plant height,the number of sympodial branches,boll number,and GOT.Plant height,monopodial branches,GOT,boll weight,seeds per boll,and short fiber index exerted direct positive effects on seed cotton yield.The first 6 principal component analysis(PCs)out of the total fourteen PCs displayed eigenvalues(>1)and had maximum share to total variability(82.79%).The attributes that had maximum share to total divergence in eluded plant height,uniformity index,the nu mber of sympodial branches,seed per boll,GOT,seed cotton yield,and short fiber index.Conclusion:The genotype AA-802,IUB-13,FH-159,FH-458,and CIM-595 were genetically diverse for most of the yield and fiber quality traits and could be utilized for the selection of better performing genotypes for further improvement.

QTL and genetic analysis controlling fiber quality traits using paternal backcross population in upland cotton

Background:Genetic improvement in fiber quality is one of the main challenges for cotton breeders.Quantitative trait loci(QTL)mapping provides a powerful approach to dissect the molecular mechanism in fiber quality traits.In present study,F14 recombinant inbred line(RIL)population was backcrossed to paternal parent for a paternal backcross(BC/P)population,deriving from one upland cotton hybrid.Three repetitive BC/P field trials and one maternal backcross(BC/M)field trial were performed including both two BC populations and the original RIL population.Results:In total,24 novel QTLs are detected for fiber quality traits and among which 13 QTLs validated previous results.Thirty-five QTLs in BC/P populations explain 5.01%–22.09%of phenotype variation(PV).Among the 35 QTLs,23 QTLs are detected in BC/P population alone.Present study provides novel alleles of male parent for fiber quality traits with positive genetic effects.Particularly,qFS-Chr3–1 explains 22.09%of PV in BC/P population,which increaseds 0.48 cN·tex−1 for fiber strength.A total of 7,2,8,2 and 6 QTLs explain over 10.00%of PV for fiber length,fiber uniformity,fiber strength,fiber elongation and fiber micronaire,respectively.In RIL population,six common QTLs are detected in more than one environment:qFL-Chr1–2,qFS-Chr5–1,qFS-Chr9–1,qFS-Chr21–1,qFM-Chr9–1 and qFM-Chr9–2.Two common QTLs of qFE-Chr2–2(TMB2386-SWU12343)and qFM-Chr9–1(NAU2873-CGR6771)explain 22.42%and 21.91%of PV.The region between NAU4034 and TMB1296 harbor 30 genes(379 kb)in A05 and 42 genes(49 kb)in D05 for fiber length along the QTL qFL-Chr5–1 in BC/P population,respectively.In addition,a total of 142 and 46 epistatic QTLs and QTL×environments(E-QTLs and QQEs)are identified in recombinant inbred lines in paternal backcross(RIL-P)and paternal backcross(BC/P)populations,respectively.Conclusions:The present studies provide informative basis for improving cotton fiber quality in different populations.

QTL Mapping for Fiber Quality Traits Based on a Dense Genetic Linkage Map with SSR,TRAP,SRAP and AFLP Markers in Cultivated Tetraploid Cotton

Cotton is one of the most important economic crops in the world,and it provides natural fiber for the textile industry.With the advancement of the textile technology and increased consumption demands on cotton fiber,both cotton yield and quality should be enhanced.However,cotton yield

Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL,significant SNP and transcriptomic data

Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL intervals,significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.Results:In our study,884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1,as a result,74 meta-QTLs were identified,including 19 meta-QTLs for fiber length;18 meta-QTLs for fiber strength;11 meta-QTLs for fiber uniformity;11 meta-QTLs for fiber elongation;and 15 meta-QTLs for micronaire.Combined with 8589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies,297 candidate genes were identified in the meta-QTL intervals,20 of which showed high expression levels specifically in the developing fibers.According to the function annotations,some of the 20 key candidate genes are associated with the fiber development.Conclusions:This study provides not only stable QTLs used for marker-assisted selection,but also candidate genes to uncover the molecular mechanisms for cotton fiber development.

Molecular Markers in Improvement of Fiber Quality Traits in Cotton

Cotton is the worlds leading natural fiber crop,and it is the cornerstone of textile industries worldwide.The cotton industry is confronted with problems in cost of production and

Analysis and identification of SCAR molecular markers associated with birch fiber length trait

The fiber length trait （FLT） of 538 individuals from nature birch population in Maorshan region, Heilongjang, China were measured, of which 100 individuals were selected as representative variety of correlated fragments screening with random amplified polymorphism DNA （RAPD） technique. In total of 20 RAPD primers were tested through multiple regression analysis between amplified strip and the character behaviors, and a correlative segment BFLR-16 was obtained. The correlation coefficient between BFLI-16 and FLT was 0.6144, with the significant level of 1%. BFLI-16 was then cloned, sequenced and transformed into SCAR marker. The percentage of identifying long fiber birches by this SCAR was more than 92. The result indicates that the SCAR markers has high specificity for the long fiber individuals and is highly linked with the gene controlling the character of fiber length, and its existence is significantly correlative with the increase in the fiber length.

QTL mapping of agronomic and economic traits for four F_(2)populations of upland cotton

Background:Upland cotton(Gossypium hirsutum)accounts for more than 90%of the annual world cotton output because of its high yield potential.However,yield and fiber quality traits often show negative correlations.We constructed four F_(2)populations of upland cotton,using two normal lines(4133B and SGK9708)with high yield potential but moderate fiber quality and two introgression lines(Suyuan04–3 and J02–247)with superior fiber quality,and used them to investigate the genetic basis underlying complex traits such as yield and fiber quality in upland cotton.We also phenotyped eight agronomic and economic traits and mapped quantitative trait loci(QTLs).Results:Extensive phenotype variations and transgressive segregation were found across the segregation populations.We constructed four genetic maps of 585.97 centiMorgan(cM),752.45 cM,752.45 cM,and 1163.66 cM,one for each of the four F_(2)populations.Fifty QTLs were identified across the four populations(7 for plant height,27 for fiber quality and 16 for yield).The same QTLs were identified in different populations,including qBW4 and qBW2,which were linked to a common simple sequence repeat(SSR)marker,NAU1255.A QTL cluster containing eight QTLs for six different traits was characterized on linkage group 9 of the 4133B×Suyuan04–3 population.Conclusions:These findings will provide insights into the genetic basis of simultaneous improvement of yield and fiber quality in upland cotton breeding.

Genetic structure,gene flow pattern,and association analysis of superior germplasm resources in domesticated upland cotton(Gossypium hirsutum L.)

Gene flow patterns and the genetic structure of domesticated crops like cotton are not well understood.Furthermore,marker-assisted breeding of cotton has lagged far behind that of other major crops because the loci associated with cotton traits such as fiber yield and quality have scarcely been identified.In this study,we used 19 microsatellites to first determine the population genetic structure and patterns of gene flow of superior germplasm resources in upland cotton.We then used association analysis to identify which markers were associated with 15 agronomic traits(including ten yield and five fiber quality traits).The results showed that the upland cotton accessions have low levels of genetic diversity(polymorphism information content=0.427),although extensive gene flow occurred among different ecological and geographic regions.Bayesian clustering analysis indicated that the cotton resources used in this study did not belong to obvious geographic populations,which may be the consequence of a single source of domestication followed by frequent genetic introgression mediated by human transference.A total of 82 maker-trait associations were examined in association analysis and the related ratios for phenotypic variations ranged from 3.04% to 47.14%.Interestingly,nine SSR markers were detected in more than one environmental condition.In addition,14 SSR markers were co-associated with two or more different traits.It was noteworthy that NAU4860 and NAU5077 markers detected at least in two environments were simultaneously associated with three fiber quality traits(uniformity index,specific breaking strength and micronaire value).In conclusion,these findings provide new insights into the population structure and genetic exchange pattern of cultivated cotton accessions.The quantitative trait loci of domesticated cotton identified will also be very useful for improvement of yield and fiber quality of cotton in molecular breeding programs.