Postharvest seed coat darkening in pinto bean (Phaseolus vulgaris) is regulated by P(sd), an allele of the basic helix‐loop‐helix transcription factor P

Pinto bean (Phaseolus vulgaris) is one of the leading market classes of dry beans that is most affected by postharvest seed coat darkening. The process of seed darkening poses a challenge for bean producers and vendors as they encounter significant losses in crop value due to decreased consumer preference for darker beans. Here, we identified a novel allele of the P gene, P(sd), responsible for the slow darkening seed coat in pintos, and identified trait‐specific sequence polymorphisms which are utilized for the development of new gene‐specific molecular markers for breeding. These tools can be deployed to help tackle this economically important issue for bean producers. SUMMARY: Postharvest seed coat darkening in pinto bean is an undesirable trait that reduces the market value of the stored crop. Regular darkening (RD) pintos darken faster after harvest and accumulate higher level of proanthocyanidins (PAs) compared to slow darkening (SD) cultivars. Although the markers cosegregating with the SD trait have been known for some time, the SLOW DARKENING (Sd) gene identity had not been proven. Here, we identified P(sd) as a candidate for controlling the trait. Genetic complementation, transcript abundance, metabolite analysis, and inheritance study confirmed that P(sd) is the Sd gene. P(sd) is another allele of the P (Pigment) gene, whose loss‐of‐function alleles result in a white seed coat. P(sd) encodes a bHLH transcription factor with two transcript variants but only one is involved in PA biosynthesis. An additional glutamate residue in the activation domain, and/or an arginine to histidine substitution in the bHLH domain of the P(sd)‐1 transcript in the SD cultivar is likely responsible for the reduced activity of this allele compared to the allele in a RD cultivar, leading to reduced PA accumulation. Overall, we demonstrate that a novel allele of P, P(sd), is responsible for the SD phenotype, and describe the development of new, gene‐specific, markers that could be utilized in breeding to resolve an economically important issue for bean producers.