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Key message <p>Through the integration of GWAS and RNA-seq analysis, three candidate genes associated with unsaturated fatty acids were identified in soybean. Heterologous overexpression of these genes in Arabidopsis confirmed their functions in altering seed fatty acid profiles.</p> <p>As a major source of the world’s vegetable oil, the nutritional value and storage stability of soybean oil are largely determined by the relative contents of unsaturated fatty acids (UFAs). However, the genetic regulations of UFAs in soybean remains incompletely understood. To elucidate the regulatory mechanisms governing UFAs in soybean seed, a panel of 312 soybean accessions was evaluated across five environments, and a genome-wide association study (GWAS) was performed to identify quantitative trait loci (QTLs) for UFA traits. A total of 52 stable QTLs were detected in at least two environments, including 20, 16 and 16 QTLs associated with oleic acid (OA), linoleic acid (LA) and linolenic acid (LNA), respectively. Of them, <i>qOA10-4</i> and <i>qLNA13-2</i> were consistently detected across four environments, while <i>qOA13-2/qLA13-1</i> and <i>qLA15-1/qLNA15-1</i> exhibited pleiotropic effects. Candidate gene analysis within 50&#xa0;kb flanking regions of lead SNPs identified 189 genes, including 61, 56 and 93 genes for OA, LA and LNA, respectively. Integrated analysis of GWAS and transcriptome data revealed 41 candidate genes showing significant differential expression between the lines with divergent UFA profiles. Sequence comparison of three prioritized candidates, <i>GmABH</i>, <i>GmCFE</i>, and <i>GmPI-PLC</i>, identified a key non-synonymous SNP in the <i>GmABH</i> coding region and promoter variations in all three candidates. Heterologous overexpression in <i>Arabidopsis</i> confirmed that all three candidate genes significantly altered the UFA profiles of the <i>Arabidopsis</i> seeds. The QTLs and candidate genes identified in this study might be useful for the improvement of UFAs in soybean.</p>

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Genome-wide association study and transcriptomic analysis reveal new genes for unsaturated fatty acid contents in soybean

  • 期刊论文

  • 发表日期：

    2026年1月25日

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  • Runqing Duan,
  • Junqi Liu,
  • Yanan Dai,
  • Ran Duan,
  • Liang Dong,
  • Yinghua Sheng,
  • Qingwei Zhang,
  • Huibing Huang,
  • Yinyue Zhao,
  • Liang Zhang,
  • Xianzhi Wang

摘要

Key message

Through the integration of GWAS and RNA-seq analysis, three candidate genes associated with unsaturated fatty acids were identified in soybean. Heterologous overexpression of these genes in Arabidopsis confirmed their functions in altering seed fatty acid profiles.

As a major source of the world’s vegetable oil, the nutritional value and storage stability of soybean oil are largely determined by the relative contents of unsaturated fatty acids (UFAs). However, the genetic regulations of UFAs in soybean remains incompletely understood. To elucidate the regulatory mechanisms governing UFAs in soybean seed, a panel of 312 soybean accessions was evaluated across five environments, and a genome-wide association study (GWAS) was performed to identify quantitative trait loci (QTLs) for UFA traits. A total of 52 stable QTLs were detected in at least two environments, including 20, 16 and 16 QTLs associated with oleic acid (OA), linoleic acid (LA) and linolenic acid (LNA), respectively. Of them, qOA10-4 and qLNA13-2 were consistently detected across four environments, while qOA13-2/qLA13-1 and qLA15-1/qLNA15-1 exhibited pleiotropic effects. Candidate gene analysis within 50 kb flanking regions of lead SNPs identified 189 genes, including 61, 56 and 93 genes for OA, LA and LNA, respectively. Integrated analysis of GWAS and transcriptome data revealed 41 candidate genes showing significant differential expression between the lines with divergent UFA profiles. Sequence comparison of three prioritized candidates, GmABH, GmCFE, and GmPI-PLC, identified a key non-synonymous SNP in the GmABH coding region and promoter variations in all three candidates. Heterologous overexpression in Arabidopsis confirmed that all three candidate genes significantly altered the UFA profiles of the Arabidopsis seeds. The QTLs and candidate genes identified in this study might be useful for the improvement of UFAs in soybean.