基于全基因组关联分析挖掘野生大豆蛋白含量QTL

Detecting QTL Underlying Wild Soybean Protein Content Through Genome Wide Association Study

为了充分挖掘野生大豆种质资源中的高蛋白基因及其连锁标记,以来自中国、韩国和日本,涵盖第4,5,6,7,8熟期组的508份野生大豆种质资源为材料,通过全基因组关联分析挖掘与野生大豆中高蛋白基因相关的SNP。参试材料蛋白含量数据从美国农业部种质资源信息网下载,为2 a利用凯氏定氮法测定蛋白含量数据平均值,基因型数据从Soybase网站下载,利用Illumina公司大豆50K芯片(SoySNP50K BeadChip含有52041个SNP标记)检测获得。结果表明,参试材料蛋白含量呈正态分布,介于38.1%~56.9%,平均48.1%,标准差2.71%。遗传结构分析将参试材料划分为3组,分别包含271,111,126份材料。基于混合线性模型的关联分析,共检测到与蛋白含量相关的SNP位点74个,散布在19条染色体的60个单倍型区段内。显著性SNP位点LOD平均值为3.47,SNP位点BARC_1.01_Gm_01_54656209_A_G的LOD值最大,为5.18。根据显著性SNP位点富集程度,确定第11号染色体常染色质区15128832~15253199 bp、第12号染色体异染色质区26842687~27818244 bp的单倍型区段为本研究中的2个蛋白含量显著性相关区段,命名为HAP_11_1和HAP_12_1。HAP_11_1中,SNP位点BARC_1.01_Gm_11_15167305_G_A的LOD值最大,为3.80,可解释遗传变异为2.88%。HAP_12_1中,SNP位点BARC_1.01_Gm_12_27563620_C_T的LOD值最大,为4.12,可解释遗传变异为3.23%。为野生大豆高蛋白基因育种利用提供了检测标记,为野生大豆高蛋白基因克隆提供了线索。

Wild soybean was useful gene pool for soybean protein content improvement.In order to detect the QTL underlying wild soybean protein content through genome wide association study,508 wild soybean accessions,collected from China,Korea and Japan and covered mature group Ⅳ,Ⅴ,Ⅵ,Ⅶ and Ⅷ,were evaluated for protein content using Kjeldahl method in two years,as well genotyped using Illumina Infinium SoySNP50K BeadChip consisting of 52041 SNPs in the present study.The phenotypic data was download at Germplasm Resources Information Network and the genotypic data was download at Soybase.As results,the protein content of the wild soybean accessions showed normal distribution,ranging from 38.1% to 56.9%,with the average 48.1%(SD=2.71%).Based on the STRUCTURE analysis,the 508 wild soybean accessions could be divided into three groups.There were 271,111,126 accessions were deposited in 3 groups,respectively.Totally,74 SNPs associated with protein scattered on 19 chromosomes were identified via MLM method.The 74 SNPs belonged to 60 haplotype blocks.The average LOD of the 74 SNPs was 3.47,and BARC_1.01_Gm_01_54656209_A_G yield the highest LOD 5.18.Two genomic regions were considered as the reliable genomic region since they yield more significant SNP in one haplotype block.The first region(named as HAP_11_1)was from 15128832 bp to 15253199 bp on chromosome 11.BARC_1.01_Gm_11_15167305_G_A was the SNP that yielded highest LOD(3.80)at HAP_11_1,and it explained 2.88% of the phenotypic variation.The second one(named as HAP_12_1)was from 26842687 bp to 27818244 bp on chromosome 12.The LOD of BARC_1.01_Gm_12_27563620_C_T was 4.12,the highest one at HAP_12_1,and this SNP explained 3.23% of the phenotypic variation.The SNPs discovered in this study were helpful to introduce high protein content related gene from wild soybean to cultivated soybean via MAS.