Denning-James Kate E, Chater Caspar, Cortés Andrés J, Blair Matthew W, Peláez Diana, Hall Anthony, De Vega José J
Earlham Institute, Norwich, NR4 7UZ, UK.
Royal Botanic Gardens, Kew, Richmond TW9 3AE, UK.
G3 (Bethesda). 2025 Jun 4;15(6). doi: 10.1093/g3journal/jkaf090.
The common bean (Phaseolus vulgaris L.) is a legume pulse crop that provides significant dietary and ecosystem benefits globally. We investigated 2 key traits, determinacy and photoperiod sensitivity, that are integral to its management and crop production, and that were early selected during the domestication of both Mesoamerican and Andean gene pools. Still, significant variation exists among common bean landraces for these traits. Since landraces form the basis for trait introgression in prebreeding, understanding these traits' genetic underpinnings and relation with population structure is vital for guiding breeding and genetic studies. We explored genetic admixture, principal component, and phylogenetic analyses using whole-genome sequencing to define subpopulations and gene pools. We used genome-wide association mapping (GWAS) to identify marker-trait associations in a diversity panel of common bean landraces. We observed a clear correlation between these traits, gene pool, and subpopulation structure. We found extensive admixture between the Andean and Mesoamerican gene pools in some regions. We identified 13 QTLs for determinacy and 10 QTLs for photoperiod sensitivity and underlying causative genes. Our study identified known and novel causative genes and a high proportion of pleiotropic effects for these traits in common bean, and likely translatable to other legume species.
普通菜豆（Phaseolus vulgaris L.）是一种豆科豆类作物，在全球范围内提供了重要的饮食和生态系统效益。我们研究了两个关键性状，即有限生长习性和光周期敏感性，它们对于其管理和作物生产至关重要，并且在中美洲和安第斯基因库的驯化过程中很早就被选择了。然而，普通菜豆地方品种在这些性状上仍存在显著差异。由于地方品种是预育种中性状渐渗的基础，了解这些性状的遗传基础以及与群体结构的关系对于指导育种和遗传研究至关重要。我们使用全基因组测序探索了遗传混合、主成分和系统发育分析，以定义亚群和基因库。我们使用全基因组关联图谱（GWAS）在普通菜豆地方品种的多样性面板中鉴定标记-性状关联。我们观察到这些性状、基因库和亚群结构之间存在明显的相关性。我们发现在某些地区，安第斯和中美洲基因库之间存在广泛的混合。我们鉴定出了13个控制有限生长习性的QTL和10个控制光周期敏感性的QTL以及潜在的致病基因。我们的研究在普通菜豆中鉴定出了已知和新的致病基因以及这些性状的高比例多效性效应，并且可能适用于其他豆科物种。
