A candidate gene marker at the red kidney color locus (Rk) enables the development of slow-darkening pink beans

Authors: OSBORNE, CAROLINE - North Dakota State University; MCCLEAN, PHIL - North Dakota State University; SOLER-GARZON, ALVARO - Washington State University; OLADZAD-NEJAD, ATENA - Cargill Corporation; LEE, RIAN - North Dakota State University; Miklas, Phillip; OSORNO, JUAN - North Dakota State University; Faris, Justin; ROY, JAYANTA - North Dakota State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/1/2026
Publication Date: 5/20/2026
Citation: Osborne, C., McClean, P., Soler-Garzon, A., Oladzad-Nejad, A., Lee, R., Miklas, P.N., Osorno, J., Faris, J.D., Roy, J. 2026. A candidate gene marker at the red kidney color locus (Rk) enables the development of slow-darkening pink beans. Theoretical and Applied Genetics. 139. Article 157. https://doi.org/10.1007/s00122-026-05256-z.
DOI: https://doi.org/10.1007/s00122-026-05256-z

Interpretive Summary: Many U.S. dry bean market classes including pinto, cranberry, light red kidney, and pink suffer from post-harvest seed coat darkening which reduces marketability. A gene p-sd that reduces seed coat darkening, has been widely deployed in pinto bean cultivars in the U.S., because it drastically improves seed appearance and marketability. Efforts to move p-sd into other market classes to delay post-harvest darkening have been unsuccessful to date. In this study we developed a marker-assisted selection strategy for breeding pink beans with the slow darkening trait. Traditional pink bean cultivars were crossed with a slow darkening pinto bean and progeny from those crosses were selected for three markers associated with genes effecting pink color (rk-p), solid nonpatterned seed coat color (pi), and slow darkening (p-sd). From 2172 progeny generated, this strategy identified 32 that were true breeding for slow darkening pink beans with commercial seed appearance. The advanced pink lines from this study with the best agronomic traits (yield, maturity) and slow-darkening seed coat trait will be used by breeders to improve seed quality and marketability of pink beans produced in the U.S.

Technical Abstract: Common bean (Phaseolus vulgaris L.) is a globally important and nutritious crop with diverse market classes. Multiple genes control the seed coat color and patterns that characterize these market classes. Therefore, understanding the genetic control of seed coat color is critical for breeding purposes, especially when making crosses among different market classes. One such gene is Rk, the “red kidney” color gene. The recessive rkp allele controls the characteristic color expression of the pink market class. Through GWAS analysis, sequencing a candidate Rk gene across multiple market classes, and genetic mapping, we determined the gene model PvUI111.02G213800, which encodes anthocyanidin reductase, is the most likely candidate for the Rk gene. Pink beans, along with several other market classes, suffer from postharvest seed coat darkening, a quality issue that cause significant economic losses and reduces consumer appeal and nutritional value. The recessive Psd allele present in some pinto genotypes imparts a “slow-darkening” (SD) phenotype. To introduce the Psd allele into the pink market class, crosses were made between three pink beans and the SD pinto cultivar ND Palomino. Among 2,240 F2 plants screened using PACE markers targeting multiple genes (Psd, rkp, and pi), including those that control pink color and slow-darkening, 32 individuals exhibited the desired alleles and SD pink genotype. The SD phenotype was verified via ultra-violet (UV) testing (' = 254 nm) and field trials of F5 generation lines demonstrated their phenotypic stability. Parallel efforts are underway to incorporate the SD trait into light red kidney and cranberry beans, broadening its utility across market classes.