ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Breeding
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1590571
Genome-wide association study for ashy stem blight resistance in USDA common bean germplasm
Provisionally accepted
- 1University of Arkansas, Fayetteville, United States
- 2University of Puerto Rico, San Juan, Puerto Rico
- 3University of Minnesota Twin Cities, St. Paul, Minnesota, United States
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Ashy stem blight (ASB), caused by the fungus Macrophomina phaseolina (Tassi) Goidanich, poses a significant threat to common bean (Phaseolus vulgaris L.) cultivation worldwide. Due to the limited Effectiveness of fungicides against ASB, the development of genetically resistant cultivars offers an eco-friendly and sustainable management strategy. This study aimed to accelerate genetic improvement in common bean by integrating molecular breeding tools with conventional breeding approaches to enhance ASB resistance. A total of 335 common bean germplasm accessions from the USDA GRIN collection were evaluated for their response to the PRI21 M. phaseolina isolate. A genome-wide association study (GWAS) was conducted using 87,193 high-quality single nucleotide polymorphisms (SNPs) and four statistical models—BLINK, MLMM, MLM, and GLM—implemented in GAPIT 3. Twenty-three accessions had intermediate resistance, with Andean PI 173208 and PI 264786 showing the lowest disease severity scores (< 3.7) to PRI21. Four quantitative trait loci (QTL) were identified on chromosomes Pv02, Pv04, Pv05, and Pv10 across all accessions. Additionally, three QTLs were detected on Pv01, Pv02, and Pv11 in Mesoamerican accessions, while three QTLs were found on Pv02, Pv04, and Pv06 in Andean accessions. The two candidate genes Phvul.002G046300 (Leucine-rich repeat [LRR] family protein) and Phvul.002G046500 (receptor-like protein kinase 1) were identified on chromosome Pv02 as being associated with ASB resistance. These SNP markers linked to these QTLs may be valuable for marker-assisted selection in common bean breeding programs aimed at improving ASB resistance.
Keywords: Ashy stem blight, common bean, Macrophomina phaseolina, Phaseolus vulgaris, Quantitative Trait Loci, Genome-Wide Association Study
Received: 09 Mar 2025; Accepted: 27 Apr 2025.
Copyright: © 2025 Shi, Viteri, Linares-Ramirez, Xiong and Chen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Ainong Shi, University of Arkansas, Fayetteville, United States
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