Table_9_Identification and Validation of Major QTLs, Epistatic Interactions, and Candidate Genes for Soybean Seed Shape and Weight Using Two Related RIL Populations.XLSX

Understanding the genetic mechanism underlying seed size, shape, and weight is essential for enhancing soybean cultivars. High-density genetic maps of two recombinant inbred line (RIL) populations, LM6 and ZM6, were evaluated across multiple environments to identify and validate M-QTLs as well as identify candidate genes behind major and stable quantitative trait loci (QTLs). A total of 239 and 43 M-QTLs were mapped by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM) approaches, from which 180 and 18, respectively, are novel QTLs. Twenty-two QTLs including four novel major QTLs were validated in the two RIL populations across multiple environments. Moreover, 18 QTLs showed significant AE effects, and 40 pairwise of the identified QTLs exhibited digenic epistatic effects. Thirty-four QTLs associated with seed flatness index (FI) were identified and reported here for the first time. Seven QTL clusters comprising several QTLs for seed size, shape, and weight on genomic regions of chromosomes 3, 4, 5, 7, 9, 17, and 19 were identified. Gene annotations, gene ontology (GO) enrichment, and RNA-seq analyses of the genomic regions of those seven QTL clusters identified 47 candidate genes for seed-related traits. These genes are highly expressed in seed-related tissues and nodules, which might be deemed as potential candidate genes regulating the seed size, weight, and shape traits in soybean. This study provides detailed information on the genetic basis of the studied traits and candidate genes that could be efficiently implemented by soybean breeders for fine mapping and gene cloning, and for marker-assisted selection (MAS) targeted at improving these traits individually or concurrently.

解析大豆籽粒大小、形状与粒重的遗传机制，对大豆品种改良具有重要意义。本研究针对LM6与ZM6两个重组自交系（recombinant inbred line, RIL）群体构建的高密度遗传图谱开展多环境表型鉴定，以挖掘并验证主效数量性状基因座（quantitative trait loci, QTLs），同时定位控制重要稳定QTL的候选基因。通过复合区间作图法（composite interval mapping, CIM）与基于混合线性模型的复合区间作图法（mixed-model-based composite interval mapping, MCIM），分别定位到239个与43个主效QTLs，其中180个与18个为新发现的QTLs。在两个重组自交系群体的多环境试验中，共验证了22个QTLs，包含4个新的主效QTLs。此外，18个QTLs表现出显著的加性×环境互作效应，40对已鉴定的QTLs呈现双基因上位性效应。本研究首次报道了34个与籽粒扁平指数（seed flatness index, FI）相关的QTLs。在大豆第3、4、5、7、9、17、19号染色体的基因组区域内，共鉴定得到7个QTL簇，每个簇均包含多个调控籽粒大小、形状与粒重的QTLs。对上述7个QTL簇所在的基因组区域进行基因注释、基因本体（gene ontology, GO）富集分析与RNA测序（RNA-seq）分析，最终筛选得到47个调控籽粒相关性状的候选基因。这些基因在籽粒相关组织与根瘤中高表达，可作为调控大豆籽粒大小、粒重与形状性状的潜在候选基因。本研究为相关性状的遗传基础解析提供了详实的理论信息，可为大豆育种工作者开展精细定位、基因克隆以及针对上述性状的单性状或多性状聚合标记辅助选择（marker-assisted selection, MAS）提供高效的指导依据。