Genome-wide Association Study (GWAS) For Yield Traits Based On RNA-Seq In Wheat

Wheat has the largest total cultivated area,the widest distribution and the highest total yield in the world.Wheat is one of the main food crops in China and plays an important role in food security.In this study,the field trails were carried out in two growing seasons using a variety population(VP)comprise of 149 wheat varieties planted latterly in the Yellow&Huai River Valley Facultative Winter Wheat Region.A number of nine yield traits including plant height(PH),spike length(SL),total spikelet number per spike(TSS),top sterile spikelet number per spike(TSSS),bsterile spikelet number per spike(BSSS),fertile spikelet number per spike(FSS),grain number per spike(GNS),spike number per m~2(SN)and grain yield(GY)were mensurated.Combining with the molecular markers come from the RNA-Seq by our group,the genome-wide association study(GWAS)were conducted for yield traits.The results should be helpful for marker associated selection(MAS)in wheat breeding programs and candidate gene isolation.The main results are as follows:The analysis of variation showed that the nine traits were obviously with the range of5.47%-65.63%.Analysis of variance(ANOVA)showed that the variances of the nine yield traits were all significant both for genotypes and environments.The broad-sense heritability ranged form 60.7%to 96.05%.A number of 369300 single nucleotide polymorphisms(SNPs)and Insertion and deletion polymorphisms(InDels)were obtained after filtrated with the standard of MAF?5%and miss rate?80%.The population structure analysis by structure2.3.4 software using 1320SNPs distributed uniformly on chromosomes indicated that?K peak value were appear when K=2,and two sub-population were confirmed which included 33 and 116 varieties,respectively.The GWAS analysis showed that 1215 SNPs/InDels were significant correlated with the nine yield traits at P<5.0E-04 level.For PH,180 SNPs/InDels were significant.Of these,nine SNPs were significant under three environments and 66 SNPs/InDels under rwo environments.For SL,120 SNPs/InDels were significant.Of these,one InDel and 13 SNPs were significant under three environments and 33 SNPs/InDels under two environments.For TSS,85SNPs/InDels were significant.Of these,five SNPs were significant under two environments.For TSSS,270 SNPs/InDels were significant.Of these,three InDels and 13 SNPs were significant under three environments and two InDels and 72 SNPs under rwo environments.For BSSS,93 SNPs/InDels were significant.Of these,two InDels and nine SNPs were significant under two environments.For FSS,97 SNPs/InDels were significant.Of these,three InDels and 12 SNPs were significant under two environments.For GNS,91SNPs/InDels were significant.Of these,22 SNPs were significant under three environments and two InDels and 14 SNPs under two environments.For SN,146 SNPs/InDels were significant.Of these,one InDel was significant under three environments and 36 SNPs under two environments.For GY,178 SNPs/InDels were significant.Of these,11 InDels and 67SNPs were significant under three environments and three InDels and 34 SNPs under two environments.