Old gene P with a new function: Psd, proanthocyanidin accumulation and postharvest seed coat darkening in pinto bean.

Postharvest seed coat darkening affects the value of pinto beans (Phaseolus vulgaris), one of the leading market classes of dry beans worldwide. Bean producers and vendors encounter significant crop value loss due to the decreased consumer preference for darker beans, poor canning quality, longer cooking time, and higher storage costs. Thus, the identification of the gene/s responsible for seed coat darkening in pinto beans was demanded to address this agro-economic issue. Seed coat darkening is caused by an elevated accumulation and oxidation of a plant specialized metabolite, proanthocyanidins (PAs). Using multiple Omics approaches and inheritance study, we identified a unique allele of the P (Pigment) gene, Psd, responsible for the slow darkening seed coat phenotype. P encodes for a bHLH transcription factor protein, and regulates late proanthocyanidin biosynthetic genes by forming MBW (MYB-bHLH-WD40) complex. To further explore seed coat darkening mechanism the interacting MYB and WD40 partners of P protein were identified by sequence analysis, protein-protein interaction and complementation assays. Thereafter, protein complexes were introduced in pinto bean hairy root system and the subsequent effect on the expression levels of target genes expression was observed for activation, which were otherwise absent in the hairy root tissues. A promoter analysis using a luciferase gene reporter system also identified the tentative binding site of MBW complex in PA late biosynthetic genes. Understanding the committed steps of PA pathway will not only benefit bean breeders to tackle the postharvest darkening issue but also allow to incorporate multiple qualitative and quantitative traits to produce improved pinto bean varieties.