Genome-wide Association Study For Economically Important Traits And Exploration Elite Alleles In Upland Cotton

Since upland cotton was introduced into China during the 1920s-1950s,hundreds of inbreed cultivars have been developed.At present,the production of upland cotton accounted for 90%of the total cotton production in China.In this study,503 inbred cultivars developed in China and some foreign cultivars from the United States and the Soviet Union were collected,which were planted and identified the phenotype of the fiber quality and yield-related traits in 8 environments(in Shihezi,North Xinjiang,Kuerle,South Xinjiang,Yuanyang,Henan and Huanggang,Hubei in 2012 and 2013),respectively.Programming language R was applied to make boxplot for phenotypic traits in different environments.Molecular diversity,linkage disequilibrium and population structure were analyzed by 494 genome-wide SSRs(Simple Sequence Repeats).Associated studyfor the fiber quality and yield-related traits were based on MLM(Mixed linear model)(G+Q+K)using TASSEL software.The elite alleles and typical materials identified based on phenotypic effect values were applied in molecular design breeding.The main results were as follows:1.A total of 179 markers were polymorphic and generated 426 allele loci,the average genetic diversity index was 0.377,rangingfrom 0.012 to 0.893;the average of polymorphism information content(PIC)was 0.336,rangingfrom 0.012 to 0.887.2.The population of 503 cultivars was divided into seven groups based on analysis of PCA,Nei's genetic distance clustering and K values used by STRUCTURE software.Clusters werecorresponded to pedigree origin,ecological and geographical distribution.3.Four hundred twenty-six SSR marker polymorphic loci formed 11628 pairs of combination loci between two linkage disequilibrium,the loci with higher level of LD were distributed on chr1,2,15,19,21,24,26;When r2<0.03 and D'= 0.25,the attenuation distance of linkage disequilibrium dropped significantly up to 0-5 cM.4.According to the comprehensive analysis of BLUP phenotypic data from six fiber quality and ten yield-related traits in eight environments.For six fiber quality traits,the range of coefficient of variationwere 0.80%(FU)-9.31%(FE);the broad sense heritability were 84%(SF)-93%(FUHML).For yield related traits,the range of coefficient of variation and broad sense heritability were 2.85%(WPG)-12.31%(FFSH),and 46%(FSBN)-93%(LP),respectively.The change trend of six fiber quality and ten yield-related traits in eight environments showed relative stably.5.Four hundred twenty-six polymorphic loci were associated with six fiber quality and ten yield-related traits based on MLM(G+Q+K).Fiber quality association showed that 216 significant marker loci(P<0.05)explained 0.58%(MON_DPL0042b)-5.12%(NAU3084c)of the phenotypic variation,with an average of 2.70%,and 27 marker loci(6.34%)were detected at P<0.01.Twenty-one marker loci were coincident with other studies,and eight were detected for the same trait.Seven quantitative trait loci were related to known genes in fiber development.Based on phenotypic effects,48 typical materials that contained the elite allele loci related to fiber quality traits were identified.Association mapping for yield-related traits showed that 261 loci(P<0.05)were associated with yield-related traits explaining 0.48%(NAU4884aand NAU3468a)-3.89%(NAU 3377db)of the phenotypic variation,with an average of 1.30%,and 54 marker loci(20.69%)were identified at P<0.01.Forty-one marker loci were coincident with other studies,and eleven were detected for the same trait.Based on phenotypic effects,44(positive effect)and 62(positive effect)typical materials(one material associated with more than 5 traits)that contained the elite allele loci related to yield-related traits were identified.6.From the first to the forth breeding stage,the phenotypic effect of 29 marker loci showed increasing trend,and 26 marker loci showed decreasing trend.Amont the loci,NAU3607a(SW and LW),MON_CGR5399c(LW and FP),MON_DPL0544(FFSBN,FP,WGP)showed increasing trend for several yield-related traits simultaneously,but NAU2858a(SW and WGP),NAU3774a(LW and LP),HAU0197a(LP and FSBN),NAU3966b(EBN.FP.WGP)and MON_CGR5866a(FFSBN and WGP)showed decreasing trend.