Shi Ainong, Xiong Haizheng, Michaels Thomas E, Chen Senyu
Department of Horticulture, University of Arkansas, Fayetteville, AR, United States.
Department of Horticultural Science, University of Minnesota, St Paul, MN, United States.
Front Plant Sci. 2025 Mar 21;16:1520087. doi: 10.3389/fpls.2025.1520087. eCollection 2025.
Soybean cyst nematode (SCN), ines, has become a significant threat in common bean () production, particularly in regions like the upper Midwest USA. Host genetic resistance offers an effective and environmentally friendly approach to managing SCN. This study aimed to conduct a genome-wide association study (GWAS) and genomic prediction for resistance to SCN HG Types 7 (race 6), 2.5.7 (race 5), and 1.3.6.7 (race 14) using 0.7 million whole-genome resequencing-generated SNPs in 354 USDA worldwide common bean germplasm accessions. Among these, 26 lines exhibited resistance to all three HG types, with a female index (FI) of less than 10. Four QTL regions on chromosomes (Chr) 2, 3, 6, and 10 were associated with resistance to HG Type 7; four regions on Chrs 2, 6, 9, and 11 were associated with resistance to HG Type 2.5.7; and three regions on Chrs 2, 6, and 10 were associated with resistance to HG Type 1.3.6.7. Cross-prediction revealed high prediction ability (PA) of 75% (r-value) for resistance to each of the three HG types. However, low PA was observed for SCN resistance through across-population prediction between the two domestications, Mesoamerican and Andean common bean accessions. Yet, using a population of mixed Mesoamerican and Andean accessions as a training set showed a high PA to predict either sub-population. This study provides SNP markers for marker-assisted selection and high PA for genomic selection in common bean molecular breeding, enabling the selection of lines and plants with high SCN resistance. Moreover, the study observed high PA for resistance among the three HG types. Interestingly, the most highly associated SNP markers and QTL for SCN resistance varied between the two domestications, and SCN resistance is more associated with the Mesoamerican domestication than the Andean domestication. This result suggests that resistance to SCN in common bean may be related to domestication rather than co-evolution with SCN.
大豆胞囊线虫（SCN）已成为普通菜豆生产中的重大威胁，尤其是在美国中西部上游地区等区域。寄主遗传抗性为管理SCN提供了一种有效且环保的方法。本研究旨在利用354份美国农业部全球普通菜豆种质资源中通过全基因组重测序产生的70万个单核苷酸多态性（SNP），对普通菜豆抗SCN HG类型7（小种6）、2.5.7（小种5）和1.3.6.7（小种14）进行全基因组关联研究（GWAS）和基因组预测。其中，26个品系对所有三种HG类型均表现出抗性，雌虫指数（FI）小于10。2号、3号、6号和10号染色体上的4个数量性状位点（QTL）区域与抗HG类型7相关；2号、6号、9号和11号染色体上的4个区域与抗HG类型2.5.7相关；2号、6号和10号染色体上的3个区域与抗HG类型1.3.6.7相关。交叉预测显示，对三种HG类型中每一种的抗性预测能力（PA）高达75%（r值）。然而，通过中美洲和安第斯普通菜豆两个驯化群体之间的跨群体预测，观察到SCN抗性的PA较低。不过，使用中美洲和安第斯群体混合的群体作为训练集显示出对任一亚群体进行预测的高PA。本研究为普通菜豆分子育种中的标记辅助选择提供了SNP标记，并为基因组选择提供了高PA，从而能够选择具有高SCN抗性的品系和植株。此外，该研究观察到对三种HG类型抗性的高PA。有趣的是，两种驯化群体中与SCN抗性相关性最高的SNP标记和QTL有所不同，并且SCN抗性与中美洲驯化的相关性高于与安第斯驯化的相关性。这一结果表明，普通菜豆对SCN的抗性可能与驯化有关，而非与SCN的协同进化有关。
