A genome-wide association study of seed size, protein content, and oil content using a natural population of Sichuan and Chongqing soybean
A genome-wide association study of seed size, protein content, and oil content using a natural population of Sichuan and Chongqing soybean
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利用川渝大豆自然群体进行种子大小、蛋白质含量和含油量的全基因组关联研究
DOI：
10.1007/s10681-021-02931-8
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发表时间：
2021-11-01
期刊：
影响因子：
1.9
通讯作者：
Wang, Songhua
中科院分区：
文献类型：
--
作者：
He, Qingyuan;Xiang, Shihua;Wang, Songhua
大豆种子含有高水平的油和蛋白质，分别提供一个人饮食需求的57%和69%。虽然大豆的百粒重（100 SW）、蛋白质含量（PRC）和油分含量（OIC）等数量性状基因座已被报道，但它们的遗传控制仍不清楚。以228份代表性材料为样本，研究了川渝生态区群体（SCLBP）3个性状的QTL等位基因构成。这些在四个环境中进行了测试，并使用135个简单重复序列（SSR）和107，081个有效的单核苷酸多态性连锁（SNP）标记进行了分析。100 SW、PRC和OIC在SCLBP材料中的分布范围分别为4.82- 33.35%、36.47- 49.75%和14.68- 21.77%。3个性状的遗传力（h2）和遗传变异系数（GCV）均较高。结果表明，利用SSR标记对100 SW、PRC和OIC分别定位到26、33和31个QTL。100 SW的Sat_260等位基因在四种环境中都检测到。此外，100 SW，PRC和OIC，分别发现28，198和250位点，使用SNP和混合线性模型（MLM）。进一步的SNP单倍型分析显示，100 SW、RPC和OIC分别发现13、35和60个区块。在四种环境中同时检测到100 SW的Gm11_9895764- 9，917，646块。在这些QTL中，利用SSR和SNP两种方法同时检测到100个SW、PRC和OIC的1个、5个和7个QTL。这些QTL中的大多数与先前报道的位点重叠。而100 SW、PRC和OIC的SSR位点分别为9、11和9个，SNP位点分别为3、5和8个，未见报道。此外，Glyma.11g130800、Glyma.13g217000和Glyma.08g122600的基因被认为分别是最可能控制100 SW、PRC和OIC的基因。这些发现为大豆这三个性状的主基因加多基因混合遗传提供了证据，并为大豆的分子解剖和育种提供了对它们遗传结构的进一步理解。
Soybean seeds contain high levels of oil and protein, providing 57 and 69% of a person's dietary requirements, respectively. Although many quantitative trait loci for the 100-seed weight (100SW), protein content (PRC), and oil content (OIC) have been reported, their genetic controls in soybeans remain unclear. The QTL–allele constitution of three traits in the Sichuan and Chongqing eco-regions population (SCLBP) was studied using a representative sample composed of 228 accessions. These were tested in four environments and analyzed using 135 simple sequence repeats (SSR) and 107,081 valid single nucleotide polymorphism linkage (SNP) markers. The range of 100SW, PRC, and OIC in SCLBP accessions were 4.82–33.35, 36.47–49.75%, and 14.68–21.77%, respectively. The heritability (h2) and genetic coefficient of variation (GCV) of the three traits were high. As a result, 26, 33, and 31 QTLs were found using SSR for 100SW, PRC, and OIC, respectively. The allele of Sat_260 for 100SW was detected in the four environments. In addition, 28, 198, and 250 loci for 100SW, PRC, and OIC, respectively, were found using SNP and mixed linear model (MLM). Further SNP haplotype analysis revealed that 13, 35, and 60 blocks were found for 100SW, RPC, and OIC, respectively. The block of Gm11_9895764-9,917,646 for 100SW was simultaneously detected in the four environments. Among these QTLs, 1, 5, and 7 for 100SW, PRC and OIC were found using two methods of SSR and SNP at the same time. A majority of these QTLs overlapped with the previously reported loci. However, 9, 11, and 9 loci for 100SW, PRC, and OIC using SSR; and 3, 5, and 8 for 100SW, PRC, and OIC hadn’t been reported using SNP. Moreover, the genes of Glyma.11g130800, Glyma.13g217000, and Glyma.08g122600 were considered the most likely genes controlling 100SW, PRC, and OIC, respectively. These findings provide evidence for mixed major plus polygenes inheritance for the three traits and an extended understanding of their genetic architecture for the molecular dissection and breeding of soybeans.