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<p>Isoflavones are important secondary metabolites in soybean that contribute to plant defense, stress adaptation, and the nutritional value of soybean-derived food products. Although the enzymatic basis of isoflavone biosynthesis has been extensively characterized, the genetic architecture underlying natural variation in the isoflavone content of soybean seeds remains insufficiently understood. In this study, a genome-wide association study (GWAS) was conducted using a panel of 216 soybean accessions to identify quantitative trait loci (QTLs) and putative genes regulating six major isoflavone components: genistein, glycitin, genistin, acetyldaidzin, malonyldaidzin, and malonylgenistin. Correlation analysis revealed strong positive relationships among genistin, acetyldaidzin, malonyldaidzin, and malonylgenistin, suggesting potential co-regulation through shared biosynthetic enzymes within the isoflavonoid pathway. The GWAS identified eight significant single-nucleotide polymorphisms (SNPs) distributed across Chr. 02, 03, 05, 11, 13, and 20, corresponding to major QTLs associated with seed isoflavone biosynthesis and accumulation. Four haplotype blocks (<i>qIso.2</i>, <i>qIso.5A</i>, <i>qIso.11</i>, and <i>qIso.13</i>) exhibited distinct haplotype–trait associations, indicating their potential as promising targets for marker-assisted selection. Candidate gene mining identified six candidate genes (<i>Glyma.05g152600</i><i>, </i><i>Glyma.05g153200, Glyma.05g156000, Glyma.05g157600, Glyma.11g131800,</i> and <i>Glyma.20g179500</i>) including key regulators such as chalcone and stilbene synthases (CHS2 and CHS3), cytochrome P450s, lipoxygenases, glycosyl hydrolases, and chorismate synthase, which are important components of enzymatic and regulatory networks within the phenylpropanoid and flavonoid pathways. Overall, this study provides valuable insights into the molecular mechanisms governing isoflavone biosynthesis and accumulation in soybean seeds. The identified loci, haplotypes, and candidate genes potentially represent important molecular resources for genomic prediction, functional validation, and targeted breeding to enhance the nutritional quality of soybean cultivars.</p>

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Genetic dissection of seed isoflavone accumulation in soybean through genome-wide association mapping and candidate gene analysis

  • 期刊论文

  • 发表日期：

    2026年7月28日

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  • Sreeparna Chowdhury,
  • Byeong Hee Kang,
  • Won-Ho Lee,
  • Seo-Young Shin,
  • Da-Yeon Kim,
  • Woon Ji Kim,
  • Hae Ju Kang,
  • Seong-Hoon Kim,
  • Bo-Keun Ha

摘要

Isoflavones are important secondary metabolites in soybean that contribute to plant defense, stress adaptation, and the nutritional value of soybean-derived food products. Although the enzymatic basis of isoflavone biosynthesis has been extensively characterized, the genetic architecture underlying natural variation in the isoflavone content of soybean seeds remains insufficiently understood. In this study, a genome-wide association study (GWAS) was conducted using a panel of 216 soybean accessions to identify quantitative trait loci (QTLs) and putative genes regulating six major isoflavone components: genistein, glycitin, genistin, acetyldaidzin, malonyldaidzin, and malonylgenistin. Correlation analysis revealed strong positive relationships among genistin, acetyldaidzin, malonyldaidzin, and malonylgenistin, suggesting potential co-regulation through shared biosynthetic enzymes within the isoflavonoid pathway. The GWAS identified eight significant single-nucleotide polymorphisms (SNPs) distributed across Chr. 02, 03, 05, 11, 13, and 20, corresponding to major QTLs associated with seed isoflavone biosynthesis and accumulation. Four haplotype blocks (qIso.2, qIso.5A, qIso.11, and qIso.13) exhibited distinct haplotype–trait associations, indicating their potential as promising targets for marker-assisted selection. Candidate gene mining identified six candidate genes (Glyma.05g152600, Glyma.05g153200, Glyma.05g156000, Glyma.05g157600, Glyma.11g131800, and Glyma.20g179500) including key regulators such as chalcone and stilbene synthases (CHS2 and CHS3), cytochrome P450s, lipoxygenases, glycosyl hydrolases, and chorismate synthase, which are important components of enzymatic and regulatory networks within the phenylpropanoid and flavonoid pathways. Overall, this study provides valuable insights into the molecular mechanisms governing isoflavone biosynthesis and accumulation in soybean seeds. The identified loci, haplotypes, and candidate genes potentially represent important molecular resources for genomic prediction, functional validation, and targeted breeding to enhance the nutritional quality of soybean cultivars.