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<p>Soybean (<i>Glycine max</i> [L.] Merr.) is a widely cultivated legume crop globally, serving as a major source of plant protein and oil for human and livestock nutrition. Seed weight, a major factor determining yield, is a crucial goal of soybean breeding. However, only a limited number of target genes underlying seed weight in soybean are known so far. In the present study, a genome-wide association study (GWAS) of soybean seed weight was conducted by utilizing 562 diverse soybean accessions mainly from Huang-Huai river basin, and genotype data from GenoBaits Soybean 10&#xa0;K Bead Chip. Based on hundred-seed weight (HSW) data from 3 environments and 3 GWAS methods/models, including BLINK, FarmCPU and 3VmrMLM, a total of 87 significant SNP-HSW association signals, located on 15 chromosomes, were identified. In order to reduce false positive rates, 19 loci, which were detected in 2 or more datasets/models, were selected as stable quantitative trait locus (QTL) associated with HSW in soybean. Among the 19 QTLs, 15 were overlapped or located close to the genomic region of the known QTLs underlying HSW, seed width or thickness, and 4 were novel for HSW, and the 3 QTLs (Chr4_9871670, Chr11_27419308 and Chr19_48317911) were repeatedly detected in many studies. To mine genes of interest, GO and KEGG pathway enrichment analysis were conducted based on a total of 488 genes flanking the 19 stable QTLs, and the result showed that 4 GO and 1 KEGG pathway entry were significant at <i>P</i>-value &lt; 0.01, and only GO:0006334, the nucleosome assembly biological process, was significant at adjust <i>P</i>-value &lt; 0.01. These findings provide a valuable foundation for HSW related gene cloning, and potential markers developing for soybean breeding.</p>

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Genome-wide association study of seed weight in the Huang-Huai river basin in soybean

  • 期刊论文

  • 发表日期：

    2026年3月10日

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  • Chun Li,
  • Shiwei Wang,
  • Jingpeng Zhang,
  • Chenfang Lei,
  • Xinjun Han,
  • Yufei Ma,
  • Jinshe Wang,
  • Weiguo Lu

摘要

Soybean (Glycine max [L.] Merr.) is a widely cultivated legume crop globally, serving as a major source of plant protein and oil for human and livestock nutrition. Seed weight, a major factor determining yield, is a crucial goal of soybean breeding. However, only a limited number of target genes underlying seed weight in soybean are known so far. In the present study, a genome-wide association study (GWAS) of soybean seed weight was conducted by utilizing 562 diverse soybean accessions mainly from Huang-Huai river basin, and genotype data from GenoBaits Soybean 10 K Bead Chip. Based on hundred-seed weight (HSW) data from 3 environments and 3 GWAS methods/models, including BLINK, FarmCPU and 3VmrMLM, a total of 87 significant SNP-HSW association signals, located on 15 chromosomes, were identified. In order to reduce false positive rates, 19 loci, which were detected in 2 or more datasets/models, were selected as stable quantitative trait locus (QTL) associated with HSW in soybean. Among the 19 QTLs, 15 were overlapped or located close to the genomic region of the known QTLs underlying HSW, seed width or thickness, and 4 were novel for HSW, and the 3 QTLs (Chr4_9871670, Chr11_27419308 and Chr19_48317911) were repeatedly detected in many studies. To mine genes of interest, GO and KEGG pathway enrichment analysis were conducted based on a total of 488 genes flanking the 19 stable QTLs, and the result showed that 4 GO and 1 KEGG pathway entry were significant at P-value < 0.01, and only GO:0006334, the nucleosome assembly biological process, was significant at adjust P-value < 0.01. These findings provide a valuable foundation for HSW related gene cloning, and potential markers developing for soybean breeding.