小麦根部耐盐性状全基因组关联分析

为了解小麦耐盐相关性状的遗传机理,挖掘与小麦耐盐性显著相关的SNP位点及候选基因,本研究利用浓度200 mmol/L的NaCl溶液和正常营养液对全国300份小麦品种(系)进行耐盐性试验,并利用小麦90 K芯片对分布于小麦全基因组的16650个SNP,采用Q+K关联混合模型对小麦最长根长、根干重、根鲜重、根平均直径、根尖数、根表面积、根体积和总根长等8个根部耐盐性相关性状进行全基因组关联分析(GWAS,genome-wide association study)。研究结果表明,小麦根部性状表现出广泛的表型变异,变异系数为24.3%~50.0%,多态性信息含量(PIC,polymorphic information content)为0.170~0.562,全基因组LD衰减距离为6 Mb;群体结构分析表明,试验所用300份小麦品种(系)可分为3个亚群,亚群1包含143个(47.67%)试验材料,主要来自河南、陕西和四川;亚群2包含74个(24.67%)试验材料,主要来自北京;亚群3包含83个(27.67%)试验材料,主要来自河南。GWAS共检测到77个与小麦耐盐相关性状显著关联的SNP位点(P≤0.001),这些位点分布在小麦除6D外的20条染色体上,单个SNP位点可解释3.70%~19.45%的表型变异,其中位于1A、3A、4A、7A、3D和5D染色体上的RAC875_c13169_459等6个位点同时关联到2个或2个以上性状,贡献率为3.78%~19.45%;对77个SNP位点进行发掘,筛选到17个可能与小麦耐盐性有关的候选基因。TraesCS5B01G031800(阳离子反转运蛋白)在Na+等阳离子转运中起重要作用,TraesCS5A01G329000(防御素)可以在阻断Na+等阳离子进入过程中起作用,TraesCS2A01G079000(重复富脯氨酸细胞壁蛋白)在细胞壁的形成中起重要作用,这些候选基因可作为耐盐性重要基因。

Genome-Wide Association Study of Salt Tolerance Related Root Traits in Wheat

In order to understand the genetic basis of salt tolerance in wheat,the SNP loci and candidate genes which were significantly associated with salt tolerance were explored.Three hundreds of wheat varieties(lines)were subjected for tests of salt tolerance using 200 mmol/L NaCl and normal nutrient solution,respectively,and these varieties were genotyped with 90 K chips exploring 16650 polymorphic SNPs.The statistical analysis was performed by using the Q+K association mixing model for eight root traits including the longest root length,root dry weight,root fresh weight,average root diameter,root tip number,root surface area,root volume and total root length.The results showed that the root traits showed extensive phenotypic variation,with a coefficient of variation of 24.3%to 50.0%,and a polymorphic information content(PIC)of 0.170-0.562,as well as a genome-wide LD attenuation distance of 6 Mb.Three subgroups were suggested by population structure analysis,including:SubgroupⅠ,which included 143 genotypes(47.67%)mainly from Henan,Shaanxi,and Sichuan provinces;SubgroupⅡ,which included 74 genotypes(24.67%)mainly from Beijing;SubgroupⅢ,which is represented by 83 lines(27.67%)mainly from Henan.Seventy-seven SNP loci(P≤0.001)were detected by genome-wide association study to be significantly associated with salt tolerance traits,and they were distributed on 20 chromosomes except chromosome 6D in wheat.Each of SNPs contributed to 3.70%to 19.45%of phenotypic variation,in which 6 loci such as RAC875c13169459 on chromosomes 1A,3A,4A,7A,3D,and 5D are simultaneously associated with two or more traits,with a contribution rate of 3.78%-19.45%.Based on the physical positions of 77 SNP loci,17 candidate genes associating with wheat salt tolerance have been proposed.For example,TraesCS5B01G031800(Cation/H(+)antiporter)might play an important role in the transport of cations such as Na+;TraesCS5A01G329000(Defensin)might play a role in blocking the entry of cations such as Na+.TraesCS2A01G079000(Repetitive proline-rich cell wall protein)might function in the formation of cell walls.Collectively,these candidate genes which have been identified from this study are proposed as important genes for salt tolerance in wheat.