小麦籽粒相关性状全基因组关联分析

Genome-wide Association Analysis of Wheat Grain Related Traits

小麦籽粒大小和形态是决定产量的主要因素之一,挖掘籽粒大小和形态性状的关联位点,筛选相关候选基因对于提高小麦产量具有重要意义。本研究以国内外具有代表性的300份冬小麦自然群体为研究材料,对千粒重、粒长、粒宽、粒厚、籽粒长宽比、籽粒面积、籽粒周长、籽粒形状和籽粒饱满度等9个籽粒性状进行表型鉴定,利用小麦90 K SNP芯片进行基因型采集,通过混合线性模型(MLM+Q+K)对籽粒大小和形态性状进行全基因组关联分析。研究结果表明,小麦籽粒大小和形态性状表现出丰富的表型变异,变异系数范围3.80%~26.06%,广义遗传力在56.25%~91.98%之间。通过GWAS检测出66个与籽粒大小和形态相关的稳定关联位点(P≤0.001),分布在除3D、4D、5D外的18条染色体上,可解释3.74%~14.34%的表型变异。检测到37个与两个及以上籽粒性状关联的一因多效位点,其中3B染色体的BS00022512_51标记同时与4个籽粒性状(粒长、粒宽、粒厚和籽粒长宽比)关联,具有最大的表型贡献率(7.06%~14.34%),6D染色体的wsnp_Ex_c4480_8055475标记同时与除粒厚、籽粒形状和籽粒饱满度以外的6个籽粒性状关联,表型贡献率为3.81%~8.25%。将BS00022512_51和wsnp_Ex_c4480_8055475标记进行单倍型分析,发现位于6D染色体上的wsnp_Ex_c4480_8055475位点存在GC-Hap1、ATHap2和AC-Hap3三种单倍型,单倍型GC-Hap1为籽粒较大的高千粒重单倍型。3种单倍型的整体分布频率分别为65.58%、32.25%和2.17%,单倍型GC-Hap1在中国4个冬麦区品种(系)中被大量选育。对37个一因多效位点进行发掘,筛选到9个籽粒大小和形态性状相关的候选基因。

Grain size and morphology is one of the main factors that determine the wheat yield.It is of great significance to mine the associated loci of grain size and morphology related traits and screen related candidate genes for improving wheat yield.In this study,300 representative natural populations of winter wheat were used to identify the phenotype at nine grain traits,including 1000-grain weight,grain length,grain width,grain thickness,grain length-width ratio,grain area,grain perimeter,grain shape and grain plumpness.This collection was genotyped by 90K SNP chip,followed by genome-wide association study using mixed linear model(MLM+Q+K).The results showed that these traits showed rich phenotypic variation,with the coefficient of variation ranged from 3.80%~26.06% and the broad heritability from 56.25% to 91.98%.Sixty-six loci(P≤0.001)were detected by GWAS on 18 chromosomes except 3D,4D and 5D,explaining 3.74%~14.34%of phenotypic variation at each locus.Thirty-seven pleiotropic loci were found associating with two or more grain traits.Especially,the BS00022512_51 marker on chromosome 3B was simultaneously correlated with 4 grain traits(grain length,grain width,grain thickness and grain length-width ratio),with the largest apparent contribution rate(7.06%~14.34%).The wsnp_Ex_c4480_8055475 markers on chromosome 6D were simultaneously associated with six grain traits except grain thickness,grain shape and grain plumpness,and the phenotypic contribution rate was 3.81%~8.25%.Haplotype analysis of BS00022512_51 and wsnp_Ex_c4480_8055475 markers showed that there were three haplotypes of GC-Hap1,AT-Hap2 and AC-Hap3 in wsnp_Ex_c4480_8055475 loucs on chromosome 6D,and Haplotype GC-Hap1 is a haplotype with large grains and high 1000-grain weight.The three haplotypes accounted for 65.58% and 32.25% and 2.17%in population,respectively.Haplotype GC-Hap1 was predominant in four winter wheat regions in China.Nine candidate genes were proposed based on 37 significantly-associated multiple effect SNPs.