GWAS identifies regulators of seed and leaf morphology in common bean, revealing OFP5 as a major seed size determinant

Phaseolus vulgaris (common bean) is one of the most economically important members of the Fabaceae family and a crop of high nutritional value. Seed and leaf morphological traits are key determinants of yield, shaped by genetic and environmental factors. In this study, we characterized a diversity panel of 434 P. vulgaris accessions for morphological and colorimetric traits. Using genome-wide association studies based on both single-nucleotide polymorphisms and structural variants, we identified 73 high-confidence quantitative trait locus (QTL). In total, we present 114 candidate genes within 25 quantitative trait loci linked to seed and leaf morphology and color, including an OVATE Family Protein 5 (PvOFP5), which was functionally validated as a key regulator of seed size in common bean. We employed a heterologous approach by overexpressing the inferior (Mesoamerican) and superior (Andean) alleles of PvOFP5 in Arabidopsis thaliana wild-type and knockout lines, and confirmed the key role of PvOFP5 in determining seed area. This work provides a comprehensive atlas of genetic associations for bean morphology and color, and highlights PvOFP5 as a promising target for marker-assisted breeding aimed at optimizing seed size.