Unravelling the Genetic Architecture of Rust Resistance in the Common Bean ( Phaseolus vulgaris L.) by Combining QTL-Seq and GWAS Analysis

• Published in: Plants (Basel) 2022-03, Vol.11 (7), p.953
• Main Authors: Wu, Xinyi, Wang, Baogen, Xin, Yan, Wang, Ying, Tian, Shuo, Wang, Jian, Wu, Xiaohua, Lu, Zhongfu, Qi, Xinjiang, Xu, Liming, Li, Guojing
• Format: Article
• Language: English
• Subjects: ABC transporter; Beans; Chromosome 4; Chromosome 5; Chromosome 6; Chromosomes; common bean; Crop yield; Cultivars; Disease; Disease resistance; French beans; Genes; Genomes; Genotype & phenotype; Germplasm; GWAS; Kinases; Legumes; NBS-LRR gene; Phaseolus vulgaris; Phenotypic variations; Phylogenetics; Plant breeding; Population; Population studies; Protein kinase; Protein transport; Proteins; QTL-Seq; Quantitative trait loci; rust; Rust fungi; Single-nucleotide polymorphism; Synteny
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants11070953

The common bean ( L.) is the most important legume crop directly used for human consumption worldwide. Bean rust, caused by , is a devastating disease and usually causes severe loss of seed yield and pod quality. Deployment of resistant cultivars is the best strategy to combat this disease. However, despite being the largest snap bean-producing country, the genetic basis research of rust resistance has largely lagged in China. In this study, an RIL population and a diversity panel were evaluated for rust resistance against a purified rust isolate using a detached leaf assay. Deploying a QTL-Seq analysis in the RIL population, a 1.81 Mb interval on chromosome 4, a 2.73 Mb interval on chromosome 5 and a 1.26 Mb interval on chromosome 6 were identified as major QTLs for rust resistance, designated as , and , respectively. Through a GWAS diversity panel, 64 significant SNPs associated with rust resistance were detected, distributed in all 11 chromosomes and explaining 19-49% of the phenotypic variation. Synteny analysis showed that was validated in GWAS, but the rust QTL/SNPs detected in our study were different from the known genes, except . A total of 114 candidate genes, including the typical NBS-LRR genes, protein kinase superfamily proteins and ABC transporter family proteins, were identified and proposed as the likely candidates. The identified 17 resistant accessions will enrich the resistant germplasm resources, and the detected QTLs/SNPs will facilitate the molecular breeding of rust resistance in the common bean.