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<p>In northwestern Himalayas, common bean (<i>Phaseolus vulgaris</i> L.) is an important legume crop. The yield of the crop is significantly reduced by many diseases and pests. One of the diseases is bean mosaic caused by bean common mosaic virus (BCMV). The pathogen is found in almost all the bean-growing areas, thus causing a catastrophic loss to the crop. Due to the lack of information on the quantitative trait loci (QTLs) controlling resistance for BCMV, the present study aimed at identifying SNPs and candidate genes for BCMV resistance in common bean using genome-wide association study (GWAS). Both the kinship matrix and PCA grouped the genotypes into two main groups belonging to Andean and Mesoamerican types with obvious subdivisions within each gene pool as an admixture group. Linkage decay was observed after a 1.0-Mb distance that has practical significance for identifying significant trait association even with a fewer number of markers. GWAS identified significant SNPs located on chromosomes Pv03, Pv04, Pv06, Pv08, and scaffold 13. Significant QTLs were consistently detected in all the environments located on chromosomes Pv03, Pv04, Pv06, and Pv08. We found many SNPs that overlap with the Co-4 gene and its presence in our material is encouraging for breeding durable anthracnose-resistant cultivars for the region. The resistant sources identified for BCMV need to be used as parents in the crossing program to develop BCMV-resistant varieties.</p>

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Identification of SNPs and Genomic Regions Linked to BCMV Resistance in Common Bean (Phaseolus vulgaris L.) Using Genome-Wide Association Analysis

  • 期刊论文

  • 发表日期：

    2025年11月2日

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  • Rayees Ahmad Tantry,
  • Rajneesh Kumar,
  • Parvaze A. Sofi,
  • Bilal A. Padder,
  • Farooq A. Ahanger,
  • Javid A. Bhat,
  • Asha Nabi,
  • Mehdi Rahimi,
  • Ajaz A. Lone

摘要

In northwestern Himalayas, common bean (Phaseolus vulgaris L.) is an important legume crop. The yield of the crop is significantly reduced by many diseases and pests. One of the diseases is bean mosaic caused by bean common mosaic virus (BCMV). The pathogen is found in almost all the bean-growing areas, thus causing a catastrophic loss to the crop. Due to the lack of information on the quantitative trait loci (QTLs) controlling resistance for BCMV, the present study aimed at identifying SNPs and candidate genes for BCMV resistance in common bean using genome-wide association study (GWAS). Both the kinship matrix and PCA grouped the genotypes into two main groups belonging to Andean and Mesoamerican types with obvious subdivisions within each gene pool as an admixture group. Linkage decay was observed after a 1.0-Mb distance that has practical significance for identifying significant trait association even with a fewer number of markers. GWAS identified significant SNPs located on chromosomes Pv03, Pv04, Pv06, Pv08, and scaffold 13. Significant QTLs were consistently detected in all the environments located on chromosomes Pv03, Pv04, Pv06, and Pv08. We found many SNPs that overlap with the Co-4 gene and its presence in our material is encouraging for breeding durable anthracnose-resistant cultivars for the region. The resistant sources identified for BCMV need to be used as parents in the crossing program to develop BCMV-resistant varieties.