A single-nucleotide polymorphism in PvPW1 encoding β-1,3-glucanase 9 is associated with pod width in Phaseolus vulgaris L.

Abstract

Pod width influences pod size, shape, yield, and consumer preference in snap beans (Phaseolus vulgaris L.). In this study, we map PvPW1, a quantitative trait locus associated with pod width in snap beans, through genotyping and phenotyping of recombinant plants. We identify Phvul.006G072800, encoding the β-1,3-glucanase 9 protein, as the causal gene for PvPW1. The PvPW1^G3555 allele is found to positively regulate pod width, as revealed by an association analysis between pod width phenotype and the PvPW1^G3555C genotype across 17 bi-parental F₂ populations. 97.7% of the 133 wide pod accessions carry PvPW1^G3555, while 82.1% of the 78 narrow pod accessions carry PvPW1^C3555, indicating strong selection pressure on PvPW1 during common bean breeding. Re-sequencing data from 59 common bean cultivars identify an 8-bp deletion in the intron linked to PvPW1^C3555, leading to the development of the InDel marker of PvM436. Genotyping 317 common bean accessions with PvM436 demonstrated that accessions with PvM436²⁴⁷ and PvM436²²⁷ alleles have wider pods compared to those with PvM436²¹⁹ allele, establishing PvM436 as a reliable marker for molecular breeding in snap beans. These findings highlight PvPW1 as a critical gene regulating pod width and underscore the utility of PvM436 in marker-assisted selection for snap bean breeding.