Genome-wide association analysis of drought resistance based on seed germination vigor and germination rate at the bud stage in common bean

Abstract

Common bean (Phaseolus vulgaris L.) is an important food legume. However, drought influences its entire growth and development process and can cause yield losses. The influence of drought stress is the most severe in the bud stage. The major objective of our study was to identify a series of loci involved in drought stress response in the bud stage using association analysis. In this study, 361 common bean germplasms were used to investigate germination vigor (GV) and germination rate (GR) under distilled water and drought stress conditions. The common bean showed large variations in GV and GR, with GV ranging from 6.67 to 100% and 0 to 73.33% and GR ranging from 66.67 to 100% and 0 to 100% in distilled water and under drought stress, respectively. A genome-wide association study (GWAS) of 361 accessions was conducted using 3,724,159 single nucleotide polymorphisms (SNPs) and revealed 2 and 11 candidate SNPs associated with relative germination rate (RGR) and relative germination vigor (RGV), respectively. Three loci were collocated with loci previously reported as being related to drought tolerance. A total of 180 candidate genes were identified, many of which were related to ion transport and oxidation-reduction reactions. A major haplotype for RGV was identified on chromosome 6. These results provide new insight into the genetic basis of drought tolerance in common bean at the bud stage and provide candidate SNPs and genes that can be used to accelerate the drought tolerance improvement of common bean.