春小麦籽粒主要品质性状的全基因组关联分析

Genome-Wide Association Study of Grain Quality Related Characteristics of Spring Wheat

【目的】挖掘小麦籽粒品质性状显著相关的SNP位点及候选基因,并揭示其遗传机理,为相关基因克隆和分子标记辅助选择提供理论依据。【方法】通过检测298份国内外春小麦品种(系)5个环境下蛋白质含量、湿面筋含量、沉降值、淀粉含量、籽粒硬度、出粉率和容重等7个籽粒品质性状的表型,并结合小麦55K SNP芯片,采用Q+K关联混合模型进行全基因组关联分析(genome-wide association study,GWAS)。【结果】外引品种(系)、地方品种(系)和育成品种(系)的7个品质性状在不同环境下的变异系数分别为1.3%—13.4%、1.1%—18.6%和1.0%—13.9%。其中,外引品种(系)的蛋白质含量、湿面筋含量和沉降值的变异系数均为最高;新疆自育品种的淀粉含量、籽粒硬度和出粉率的变异系数最大,而新疆地方品种的蛋白质含量、湿面筋含量、沉降值、淀粉含量、籽粒硬度和出粉率6个品质性状的变异系数均介于外引品种(系)和新疆自育品种(系)之间。群体结构分析表明,298份小麦品种(系)可分为3个亚群。其中,亚群1包含128份(43.0%)试验材料,主要是来自新疆的地方品种(系);亚群2包含24份(8.1%)试验材料,主要包括外引品种(系)和新疆地方品种;亚群3包含146份(48.9%)试验材料,主要是外引品种(系)。连锁不平衡分析表明A、B和D基因组及全基因组的LD衰减距离分别为10、10、6和8 Mb,依据全基因组的LD衰减距离,将在物理图谱上前后8 Mb区间内的位点认定为一个候选位点。通过GWAS共检测到85个与7个小麦籽粒品质性状显著关联的稳定位点(P<0.001)贡献率为3.7%—10.9%。在1B、1D、2D、3A、3D、4A、4B、5A、6A、6D、7A和7D染色体上均检测到稳定且同时与多个性状关联的位点。其中,7A染色体上的AX-109452823—AX-110545157同时与蛋白质含量、淀粉含量、湿面筋含量、沉降值、出粉率和籽粒硬度相关,且同时在4个环境中均被检测到。对稳定的位点进行候选基因发掘,筛选到10个可能与小麦籽粒品质相关的候选基因。其中TraesCS4A01G299800(阳离子氨基酸转运蛋白)、TraesCS7A01G059500(色氨酸脱羧酶)、TraesCS7A01G331200和TraesCS7D01G418700(木葡聚糖内转葡糖基酶/水解酶)对调控小麦籽粒氨基酸含量有重要作用。【结论】检测到85个稳定的且与小麦籽粒品质性状关联的位点,并筛选出10个与小麦籽粒品质性状相关的候选基因。

【Objective】Identify SNPs and candidate genes that are significantly related to wheat grain quality traits,and reveal their genetic mechanism.【Method】In this study,298 introduced varieties(lines),Xinjiang landrace(lines)and Xinjiang bred varieties(lines)were used for an association population.Seven grain quality traits,including protein content(PRC),wet gluten content(WGC),sedimentation value(SV),starch content(STC),grain hardness(GH),flour yield(FY)and test weight(TW),were measured under five environments.Based on phenotypes of seven quality traits and genotypes of 55K SNP markers in this population,the Q+K association mixed model was used for genome-wide association analysis to obtain significantly associated SNP loci.【Result】The coefficients of variation of the seven grain quality traits of introduced varieties(lines),landraces and bred varieties(lines)under different environments were 1.3%-13.4%,1.1%-18.6%and 1.0%-13.9%,respectively.Among them,the protein content,wet gluten content and sedimentation value of introduced varieties(lines)have the highest coefficient of variation(CV);Xinjiang bred varieties(lines)have the largest CV of starch content,grain hardness and flour yield.Whereas,for other six grain quality traits,including protein content,wet gluten content,sedimentation value,starch content,grain hardness,and the coefficients of variation of Xinjiang landraces are all between those of the introduced varieties(lines)and Xinjiang bred varieties(lines).Population structure analysis showed that 298 wheat varieties(lines)can be divided into 3 subgroups.Subgroup 1 contains 128(43.0%)the materials mainly from landrace(lines);Subgroup 2 has 24(8.1%)materials,mainly including introduced varieties(lines)and landraces;Subgroup 3 contains 146(48.9%)materials,mainly introduced varieties(lines).The linkage disequilibrium analysis showed that the LD attenuation distances of the A,B and D genomes and the whole genome respectively were 10,10,6 and 8 Mb,according to the LD attenuation distance of the whole genome,the loci in the 8 Mb interval after the physical map were identified as a candidate loci.A total of 85 loci were simultaneously detected in two or more environments,that were significantly associated with 7 wheat grain quality traits detected by GWAS,with a contribution rate of 3.7%-10.9%.Stable SNPs associated with multiple traits were detected on chromosomes 1B,1D,2D,3A,3D,4A,4B,5A,6A,6D,7A and 7D.Among them,AX-109452823-AX-110545157 on chromosome 7A is related to protein content,starch content,wet gluten content,sedimentation value,flour yield and grain hardness,and was detected across four environments.Candidate genes at stable loci associated with multiple traits were searched,and 10 candidate genes that might be related to wheat grain quality were screened.Among them,TraesCS4A01G299800(cationic amino acid transporter),TraesCS7A01G059500(tryptophan decarboxylase),TraesCS7A01G331200,TraesCS7D01G418700(xyloglucan endoglucosylase/hydrolase)play important roles in regulating the amino acid content in wheat grains.【Conclusion】The 85 loci were simultaneously detected in two or more environments,and 10 candidate genes related to wheat grain quality traits were predicted.