Genome-wide association study dissecting drought resistance-associated loci based on physiological traits in common bean

Abstract

Genetic improvement of drought resistance is one of the main breeding goals for common bean; therefore, molecular markers need to be identified to facilitate drought resistance breeding. In this study, we evaluated the proline, trehalose, raffinose and stachyose contents of 210 common bean accessions under two watering conditions and found high variation. The coefficient of variation ranged from 21.21% for proline content to 78.69% for stachyose content under well-watered conditions and from 20.11% for proline content to 50.08% for trehalose content under drought stress. According to our genome-wide association analysis, 32 quantitative trait loci were associated with drought resistance, and seven overlapped with known loci. Four hotspot regions were identified at Pv01, Pv07 and Pv11. A set of candidate genes was identified, including genes encoding MYB, bZIP, bHLH, ERF and protein kinases. Among these genes, Phvul.001G189400, Phvul.007G273000 and Phvul.008G270500 were annotated as bZIP, ERF and WRKY, respectively. These genes have been reported to be involved in drought stress responses in Arabidopsis thaliana and were induced by drought stress in common bean. Significant SNPs in six candidate gene regions formed different haplotypes, and phenotypic analysis revealed significant differences among the haplotypes. These results provide new insight into the genetic basis of drought resistance in common bean and reveal candidate genes and superior natural variations that will be useful for improving common bean.