The phenotypic color of seeds is a complex agronomic trait and has economic and biological significance. The genetic control and molecular regulation mechanisms have been extensively studied. Here, we used a multi-omics strategy to explore the color formation in soybean seeds at a big data scale. We identified 13 large quantitative trait loci (QTL) for color with bulk segregating analysis in recombinant inbreeding lines. GWAS analysis of colors and decomposed attributes in 763 germplasms revealed associated SNP sites perfectly falling in five major QTL, suggesting inherited regulation on color during natural selection. Further transcriptomics analysis before and after color accumulation revealed 182 differentially expression genes (DEGs) in the five QTL, including known genes CHS, MYB, and F3′H involved in pigment accumulation. More DEGs with consistently upregulation or downregulation were identified as shared regulatory genes for two or more color formations while some DEGs were only for a specific color formation. For example, five upregulated DEGs in QTL qSC-3 were in flavonoid biosynthesis responsible for black and brown seed. The DEG (Glyma.08G085400) was identified in the purple seed only, which encodes gibberellin 2-beta-dioxygenase in the metabolism of colorful terpenoids. The candidate genes are involved in flavonoid biosynthesis, transcription factor regulation, gibberellin and terpenoid metabolism, photosynthesis, ascorbate and aldarate metabolism, and lipid metabolism. Seven differentially expressed transcription factors were also speculated that may regulate color formation, including a known MYB. The finds expand QTL and gene candidates for color formation, which could guide to breed better cultivars with designed colors.

种子的表型颜色是一种复杂的农艺性状，具有经济和生物学意义。遗传控制和分子调控机制已被广泛研究。在这里，我们使用多组学策略在大数据规模下探索大豆种子的颜色形成。我们通过重组近交系中的批量分离分析鉴定了 13 个大型颜色数量性状基因座 (QTL)。对 763 个种质的颜色和分解属性的 GWAS 分析显示，相关的 SNP 位点完全落在 5 个主要 QTL 中，表明自然选择过程中颜色的遗传调控。进一步对颜色积累前后的转录组学分析发现，5个QTL中有182个差异表达基因（DEG），包括已知的参与色素积累的基因CHS、MYB和F3'H 。更多持续上调或下调的 DEG 被确定为两种或多种颜色形成的共享调控基因，而一些 DEG 仅针对特定颜色形成。例如，QTL qSC-3中的五个上调 DEG参与类黄酮生物合成，负责黑色和棕色种子。仅在紫色种子中鉴定出DEG ( Glyma.08G085400 )，它编码彩色萜类化合物代谢中的赤霉素 2-β-双加氧酶。候选基因涉及类黄酮生物合成、转录因子调节、赤霉素和萜类化合物代谢、光合作用、抗坏血酸和醛糖酸代谢以及脂质代谢。还推测七个差异表达的转录因子可能调节颜色形成，其中包括已知的 MYB。这些发现扩大了颜色形成的 QTL 和候选基因，这可以指导培育具有设计颜色的更好品种。