Table_9_A Major and Stable Quantitative Trait Locus qSS2 for Seed Size and Shape Traits in a Soybean RIL Population.XLSX

Seed size and shape traits are important determinants of seed yield and appearance quality in soybean [Glycine max (L.) Merr.]. Understanding the genetic architecture of these traits is important to enable their genetic improvement through efficient and targeted selection in soybean breeding, and for the identification of underlying causal genes. To map seed size and shape traits in soybean, a recombinant inbred line (RIL) population developed from K099 (small seed size) × Fendou 16 (large seed size), was phenotyped in three growing seasons. A genetic map of the RIL population was developed using 1,485 genotyping by random amplicon sequencing-direct (GRAS-Di) and 177 SSR markers. Quantitative trait locus (QTL) mapping was conducted by inclusive composite interval mapping. As a result, 53 significant QTLs for seed size traits and 27 significant QTLs for seed shape traits were identified. Six of these QTLs (qSW8.1, qSW16.1, qSLW2.1, qSLT2.1, qSWT1.2, and qSWT4.3) were identified with LOD scores of 3.80–14.0 and R2 of 2.36%–39.49% in at least two growing seasons. Among the above significant QTLs, 24 QTLs were grouped into 11 QTL clusters, such as, three major QTLs (qSL2.3, qSLW2.1, and qSLT2.1) were clustered into a major QTL on Chr.02, named as qSS2. The effect of qSS2 was validated in a pair of near isogenic lines, and its candidate genes (Glyma.02G269400, Glyma.02G272100, Glyma.02G274900, Glyma.02G277200, and Glyma.02G277600) were mined. The results of this study will assist in the breeding programs aiming at improvement of seed size and shape traits in soybean.

种子大小与形状性状是决定大豆[Glycine max (L.) Merr.]种子产量及外观品质的关键因素。解析此类性状的遗传架构，可为通过大豆育种中的高效定向选择实现性状遗传改良，以及挖掘潜在的因果基因提供重要支撑。为定位大豆种子大小与形状性状，本研究以由小粒品种K099与大粒品种‘奋斗16’杂交构建的重组自交系（recombinant inbred line, RIL）群体为材料，于3个生长季开展表型鉴定。本研究利用1485个随机扩增子测序直接分型（genotyping by random amplicon sequencing-direct, GRAS-Di）标记与177个简单序列重复（simple sequence repeat, SSR）标记，构建了该RIL群体的遗传连锁图谱，并通过完备复合区间作图法开展数量性状位点（Quantitative trait locus, QTL）定位分析。最终共鉴定到53个控制种子大小性状的显著QTL，以及27个控制种子形状性状的显著QTL。其中6个QTL（qSW8.1、qSW16.1、qSLW2.1、qSLT2.1、qSWT1.2及qSWT4.3）在至少2个生长季中被检测到，其似然比对数（logarithm of odds, LOD）值介于3.80~14.0之间，表型解释率（决定系数R²）为2.36%~39.49%。在上述显著QTL中，24个QTL可被整合为11个QTL簇；例如，3个主效QTL（qSL2.3、qSLW2.1及qSLT2.1）聚集于第2号染色体上的一个主效QTL区域，将其命名为qSS2。本研究通过一对近等基因系验证了qSS2的遗传效应，并挖掘到其候选基因共5个：Glyma.02G269400、Glyma.02G272100、Glyma.02G274900、Glyma.02G277200及Glyma.02G277600。本研究结果可为以改良大豆种子大小与形状性状为目标的育种项目提供理论支撑与技术参考。