Genome-wide Scan for Seed Composition Provides Insights into Soybean Quality Improvement and the Impacts of Domestication and Breeding

Jiaoping Zhang, Xianzhi Wang, Yaming Lu, Siddhi J. Bhusal, Qijian Song, Perry B. Cregan, Yang Yen, Michael Brown, Guo Liang Jiang

Research output: Contribution to journalArticlepeer-review

104 Scopus citations


The complex genetic architecture of quality traits has hindered efforts to modify seed nutrients in soybean. Genome-wide association studies were conducted for seed composition, including protein, oil, fatty acids, and amino acids, using 313 diverse soybean germplasm accessions genotyped with a high-density SNP array. A total of 87 chromosomal regions were identified to be associated with seed composition, explaining 8%–89% of genetic variances. The candidate genes GmSAT1, AK-HSDH, SACPD-C, and FAD3A of known function, and putative MtN21 nodulin, FATB, and steroid-5-α-reductase involved in N2 fixation, amino acid biosynthesis, and fatty acid metabolism were found at the major-effect loci. Further analysis of additional germplasm accessions indicated that these major-effect loci had been subjected to domestication or modern breeding selection, and the allelic variants and distributions were relevant to geographic regions. We also revealed that amino acid concentrations related to seed weight and to total protein had a different genetic basis. This helps uncover the in-depth genetic mechanism of the intricate relationships among the seed compounds. Thus, our study not only provides valuable genes and markers for soybean nutrient improvement, both quantitatively and qualitatively, but also offers insights into the alteration of soybean quality during domestication and breeding. Molecular and genomic investigation helps to reveal the genetic architecture of complex traits. By a genome-wide association study, 138 quantitative trait loci associated with seed composition and many candidate genes were identified in soybean. The results also indicated a different genetic basis between seed-weight-based and total-protein-corrected amino acids and revealed a marked impact of soybean domestication and modern breeding selection on six major-effect loci.

Original languageEnglish (US)
Pages (from-to)460-472
Number of pages13
JournalMolecular Plant
Issue number3
StatePublished - Mar 5 2018

Bibliographical note

Funding Information:
This work was supported in part by the USDA-NIFA/CSREES Hatch project and Even-Allen project, and grants from the United Soybean Board (USB) and the South Dakota Soybean Research and Promotion Council (SDSRPC) awarded to G.-L. Jiang.

Publisher Copyright:
© 2017 The Author


  • GWAS
  • candidate genes
  • domestication and breeding
  • genome-wide association study
  • quality improvement
  • seed composition
  • soybean


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