Genetic Diversity and GWAS Analysis of Southern Africa Common Bean Panel for Acanthoscelides obtectus (Say) Resistance

Abstract Bruchid damage substantially reduces the post-harvest value of common bean, yet breeding for resistance in Southern African germplasm is constrained by limited integration of phenotypic, genomic and breeding information. This study evaluated 190 common bean genotypes for resistance to Acanthoscelides obtectus in a three-replication laboratory assay and combined the resistance phenotypes with high-density DArTseq data for genomic structure and genome-wide association analysis. Mean seed damage was 69.09%, but five genotypes combined less than 20% mean damage with no more than one mean emergence hole per seed and were identified as priority donor candidates. Entry-mean broad-sense heritability was moderate for emergence holes (H² = 0.427) and percent seed damage (H² = 0.339). Genome-wide structure was pronounced and was incorporated into association analysis. Multi-locus GWAS repeatedly prioritized Pv08 marker 3379776 at 3.155 Mb for emergence holes, while a Pv02 signal at 13.997 Mb showed a larger model-specific effect. Percent seed damage showed a more diffuse pattern involving recurrent signals on Pv03, Pv01 and Pv06. Functional annotation of the associated chromosomes identified candidate defence processes involving receptor signalling, WRKY/AP2-ERF regulation, phenylpropanoid and isoflavonoid metabolism, jasmonate-related responses, redox control and cell-wall reinforcement. These findings identify resistant breeding material and genomic regions for validation while emphasizing that marker deployment requires independent phenotypic and positional confirmation.