An omics strategy increasingly improves the discovery of genetic loci and genes for seed-coat color formation in soybean

Jian Song; Ruixin Xu; Qingyuan Guo; Caiyu Wu; Yinghui Li; Xuewen Wang; Jun Wang; Li-Juan Qiu

doi:10.1007/s11032-023-01414-z

An omics strategy increasingly improves the discovery of genetic loci and genes for seed-coat color formation in soybean

Mol Breed. 2023 Aug 31;43(9):71. doi: 10.1007/s11032-023-01414-z. eCollection 2023 Sep.

Authors

Jian Song^#¹, Ruixin Xu^#¹, Qingyuan Guo^#¹, Caiyu Wu¹, Yinghui Li², Xuewen Wang³, Jun Wang¹, Li-Juan Qiu²

Affiliations

¹ Yangtze University, Jingzhou, 434025 Hubei P.R. China.
² The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China.
³ Department of Genetics, University of Georgia, Athens, GA 30602 USA.

^# Contributed equally.

PMID: 37663546
PMCID: PMC10471558 (available on 2024-08-31)
DOI: 10.1007/s11032-023-01414-z

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.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01414-z.

Keywords: Bulk sequencing; Differential expression; GWAS; Regulation; Seed color; Soybean.

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