Tocopherol (Toc) in soybean seeds has value for foods, medicines, cosmetics, and animal husbandry. Soybean breeders and soybean-derived food industries have thus focused on breeding new soybean cultivars with higher seed Toc content. In this study, an association panel consisting of 180 diverse soybean accessions were used to detect quantitative trait nucleotides (QTNs) and scan possible candidate genes based on genome-wide association analysis (GWAS) and high-throughput single-nucleotide polymorphisms (SNP). Approximately 22,611 SNPs were identified using the specific locus amplified fragment sequencing (SLAF-seq) approach and based on minor allele frequencies (MAFs) > 5 %, which spanned 84.10 % of the soybean whole genome. For the three individuals including α-tocopherol (α-Toc), γ- tocopherol (γ-Toc), δ- tocopherol (δ-Toc), and total tocopherol (total Toc) levels, a total of 18 quantitative trait nucleotides (QTNs) distributed on the 18 genomic regions of 10 chromosomes were verified via GWAS. Seven QTNs (rs55811336, rs7975863, rs37094897, rs7097743, rs17125409, rs330000, and rs4730199) could be identified in more than three environments, and the other eleven could be identified in least two environments. A total of 6, 8, 4, and 10 QTNs were novel loci for α-Toc, γ-Toc, δ-Toc, and total Toc, respectively. Nine QTNs (rs37505279, rs37686178, rs36359429, rs6898494, rs7097743, rs17125409, rs10200201, rs21080726, and rs5680781) were associated with more than one Toc component. A total of 216 candidate genes near the 200-kb flanking region of these identified QTNs were identified as potential candidate genes associated with soybean seed Toc levels. Of these genes, Glyma.17G061900 (located near QTN rs4730199 on Chr.17), a homogentisate phytyltransferase 1 that catalytic homogentisate to 2-methyl-6-phyl-1,4-benzoquinol in Toc biosynthesis, was detected through association analysis, haplotype analysis, and expression pattern analysis. The identified QTNs with beneficial alleles and the candidate genes would be valuable for improving Toc levels in soybean seeds and improving the nutritional value of soybean oil.

大豆种子中的生育酚（Toc）对食品，药品，化妆品和畜牧业具有价值。因此，大豆育种者和大豆衍生的食品工业集中于育种具有较高种子Toc含量的新大豆品种。在这项研究中，由180种不同大豆种质组成的关联小组用于检测定量性状核苷酸（QTN），并基于全基因组关联分析（GWAS）和高通量单核苷酸多态性（SNP）扫描可能的候选基因。使用特定基因座扩增片段测序（SLAF-seq）方法并基于次要等位基因频率（MAF）> 5％，鉴定出约22,611个SNP，其覆盖了大豆整个基因组的84.10％。对于包括α-生育酚（α-Toc），γ-生育酚（γ-Toc），δ-生育酚（δ-TOC）和总生育酚（总TOC）的水平，总共18个数量性状核苷酸分布在10条染色体的18个基因组区域（QTNs）进行了验证通过GWAS。可以在三个以上的环境中识别七个QTN（rs55811336，rs7975863，rs37094897，rs7097743，rs17125409，rs330000和rs4730199），而其他十一个可以在至少两个环境中识别。共有6个，8个，4个和10个QTN分别是α-Toc，γ-Toc，δ-Toc和总Toc的新基因座。九个QTN（rs37505279，rs37686178，rs36359429，rs6898494，rs7097743，rs17125409，rs10200201，rs21080726和rs5680781）与一个以上的Toc组件相关联。在这些鉴定出的QTN的200kb侧翼区域附近共有216个候选基因被鉴定为与大豆种子Toc水平相关的潜在候选基因。在这些基因中，Glyma.17G061900（位于Chr.17上QTN rs4730199附近），通过缔合分析，单倍型分析和表达模式分析，检测到了在Toc生物合成中催化纯合为2-甲基-6-phyl-1,4-苯并喹啉的纯合植酸植酸转移酶1。鉴定出的具有有益等位基因和候选基因的QTN对提高大豆种子中的Toc含量和提高豆油的营养价值具有重要价值。