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<p>Flower color is a crucial morphological trait and evolutionary marker in soybean (<i>Glycine max</i>). However, its complex genetic architecture and domestication history remain incompletely understood. Here, we performed a genome-wide association study (GWAS) on 741 soybean accessions, comprising 411 cultivated and 330 wild accessions, using three distinct statistical models (GLM, MLM, and FarmCPU) with over 7.95 million SNPs, integrated with selective sweep and transcriptomic analyses. We identified two significant quantitative trait loci (QTLs) governing floral pigmentation. The major locus, <i>qFC13</i>, explaining 48.63% of the phenotypic variance, corresponds to the classical <i>W1</i> gene (<i>GmW82.13G060100</i>, encoding F3′5'H). It exhibits strong signatures of a hard selective sweep, driving the domestication transition from the exclusively purple flowers of wild soybeans to dimorphic variations in cultivars. Additionally, a novel candidate (<i>GmW82.13G060300</i>) was also pinpointed within the <i>W1</i> locus as a potential regulator significantly involved in the terpenoid biosynthetic pathway. Furthermore, we uncovered a novel locus, <i>qFC19</i>, explaining 6.24% of the phenotypic variation and functioning as a quantitative modifier under soft selection. Haplotype and spatiotemporal expression profiling delineated key candidate genes within <i>qFC19</i>, distinct haplotypes of these genes exhibit pronounced stratification across different soybean species and flower color phenotypes, revealing divergent distribution patterns correlated with domestication and trait variation. Ultimately, the identification of these genes defines a unique genetic foundation for soybean flower color and uncovers a complex regulatory landscape. This work advances our understanding of secondary metabolism evolution and establishes new targets for marker-assisted crop breeding.</p>

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Integrated GWAS and selective sweep analysis reveals the genetic basis of flower color variation and domestication in soybean

  • 期刊论文

  • 发表日期：

    2026年6月30日

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  • Meng Wang,
  • Bingqi Zhang,
  • Wei Zhang,
  • Fentuan Yang,
  • Hongwei Xun

摘要

Flower color is a crucial morphological trait and evolutionary marker in soybean (Glycine max). However, its complex genetic architecture and domestication history remain incompletely understood. Here, we performed a genome-wide association study (GWAS) on 741 soybean accessions, comprising 411 cultivated and 330 wild accessions, using three distinct statistical models (GLM, MLM, and FarmCPU) with over 7.95 million SNPs, integrated with selective sweep and transcriptomic analyses. We identified two significant quantitative trait loci (QTLs) governing floral pigmentation. The major locus, qFC13, explaining 48.63% of the phenotypic variance, corresponds to the classical W1 gene (GmW82.13G060100, encoding F3′5'H). It exhibits strong signatures of a hard selective sweep, driving the domestication transition from the exclusively purple flowers of wild soybeans to dimorphic variations in cultivars. Additionally, a novel candidate (GmW82.13G060300) was also pinpointed within the W1 locus as a potential regulator significantly involved in the terpenoid biosynthetic pathway. Furthermore, we uncovered a novel locus, qFC19, explaining 6.24% of the phenotypic variation and functioning as a quantitative modifier under soft selection. Haplotype and spatiotemporal expression profiling delineated key candidate genes within qFC19, distinct haplotypes of these genes exhibit pronounced stratification across different soybean species and flower color phenotypes, revealing divergent distribution patterns correlated with domestication and trait variation. Ultimately, the identification of these genes defines a unique genetic foundation for soybean flower color and uncovers a complex regulatory landscape. This work advances our understanding of secondary metabolism evolution and establishes new targets for marker-assisted crop breeding.