Abstract
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.
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The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.
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This work was supported by the National Natural Scientific Foundation of China (Grant No.: 32072016).
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All authors contributed to the study’s conception and design. Material preparation, data collection, and analysis were performed by Jian Song, Qingyuan Guo, Ruixin Xu, and Xuewen Wang. The first draft of the manuscript was written by Jian Song and Xuewen Wang. Caiyu Wu helped on the experimental treatment, and Yinghui Li conceived the mutant and provided data support. Li-Juan Qiu supervised the project and reviewed the manuscript. Jun Wang revised the manuscript. All authors read and approved the final manuscript.
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The genetic basis of soybean seed coat color by BSA mapping of segregation population and GWAS of 763 germplasms
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Song, J., Xu, R., Guo, Q. et al. An omics strategy increasingly improves the discovery of genetic loci and genes for seed-coat color formation in soybean. Mol Breeding 43, 71 (2023). https://doi.org/10.1007/s11032-023-01414-z
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DOI: https://doi.org/10.1007/s11032-023-01414-z