Linking herbicide cross‐tolerance to agronomic and seed vigor traits: A multi‐trait genome‐wide association study in snap bean ( <i>Phaseolus vulgaris</i> L.)

Abstract In snap bean ( Phaseolus vulgaris L.) production, herbicides are essential for weed control, requiring crop tolerance to avoid injury. The study aimed to link genomic loci to agronomic traits, explore the extent of herbicide cross‐tolerance, and identify loci influencing seed vigor and herbicide tolerance traits. A panel was evaluated for seven agronomic traits and two measures of tolerance to eight herbicides. Genome‐wide association studies (GWASs) identified marker‐trait associations (MTA) and candidate genes. Heritability confirmed genetic control over agronomic traits. Seed weight and traits measuring seed and at‐flowering vigor showed positive correlations. Multilocus GWAS identified 179 MTA for seven agronomic traits, with 28 regions linked to multiple traits. Candidate genes included those involved in cell wall synthesis, DNA repair and methylation, radical oxygen species scavenging, and signal transduction. Identified candidate genes related to flowering provide insights into flowering control beyond TFL 1. Positive correlation between herbicide cross‐tolerance and seed vigor traits suggests shared mechanisms. Multi‐trait GWAS identified genomic regions linked to herbicide cross‐tolerance and seed vigor traits. Across all trait groupings, 69 multi‐trait MTAs were identified. Chromosomes 1, 2, 4, and 8 regions were associated with seed vigor measures under herbicide and control conditions in multiple analyses. Favorable alleles for stress tolerance operate independently of growth habit and ancestry and were present in higher frequencies in lines with Middle American ancestry. This research highlights genetic links between herbicide tolerance and plant fitness, identifying loci associated with agronomic traits, and provides resources for breeding of snap beans with enhanced resilience and agronomic performance.