Molecular Genetic Analysis of the Phaseolus vulgaris P Locus

P locus is the “ground factor” that controls the seed coat and flower color-major descriptors of market classes in common bean. It has multiple alleles with different dominance effects; the recessive allele (p) is epistatic to other color genes and confers white color. This locus can potentially be a transcription factor that regulates the flavonoid biosynthesis pathway such as AtTT8 or Ps A gene in the MBW complex (TT2, TT8, TTG1). We identified two tandem gene models in common bean that were orthologous to AtTT8. Two tandem gene models were located near the OU3₂₃₀₀ RAPD within a 3Mb region flanked by g2416 and g1175 markers. The RNA-seq contig data demonstrated that two tandem gene models are part of a single gene and the in silico gene model prediction was incorrect. The P gene candidate was independently identified in a GWAS using the beanCAP Mesoamerican diversity panel. A penalized multiple logistic regression was used and eight significant SNPs were detected on Pv 07 within the 3Mb interval. Two markers were inside the P gene candidate and in complete LD. We found four alleles for the p candidate by screening multiple populations using a diagnostic marker that encompassed the first two exons and intron1. These molecular genetic analysis of the P locus paves the way for further in depth studies about the inheritance of this important trait in common bean.