White seed color in common bean (Phaseolus vulgaris L.) results from convergent evolution in the P (pigment) gene

Authors: MCCLEAN, PHIL - North Dakota State University; BETT, KIRSTEN - University Of Saskatchewan; STONEHOUSE, ROBERT - University Of Saskatchewan; LEE, RIAN - North Dakota State University; PFLIEGER, STEPHANIE - National Council For Scientific Research-Cnrs; MOGHADDAM, SAMIRA - North Dakota State University; GEFFROY, VALERIE - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; Miklas, Phillip - Phil; MAMIDI, SUJAN - North Dakota State University

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2018
Publication Date: 6/13/2018
Citation: McClean, P., Bett, K., Stonehouse, R., Lee, R., Pflieger, S., Moghaddam, S., Geffroy, V., Miklas, P.N., Mamidi, S. 2018. White seed color in common bean (Phaseolus vulgaris L.) results from convergent evolution in the P (pigment) gene. New Phytologist. https://doi.org/10.1111/nph.15259.
DOI: https://doi.org/10.1111/nph.15259

Interpretive Summary: Dry edible beans come in many different sizes, shapes, and colors. The seed colors range from pink, red, purple, brown, to black and many shades in between. To have color is controlled by a single gene ‘P’ (for pigment). Spontaneous mutations to the P gene knock out the color pathway resulting in white-seeded beans. Navy, great northern, white kidney, alubia, and other white-seeded dry edible bean types were all thought to derive from the same mutation of the P gene. This study characterized the P gene and found that there were many different mutations which knocked out the gene resulting in white seeded beans. This finding is important when breeding improvements in white beans as the source of the mutated P gene can affect agronomic performance in different market types. For instance the navy bean mutation is associated with smaller seed size so is not desired for breeding white kidney beans. Whereas the mutation found in great northern beans does not appear to have a negative effect on performance of navy beans. We developed markers that now allow breeders to track the different mutations affecting white seed color to help them retain the mutation best suited for improvement of the targeted market class, be it navy, great northern, etc.

Technical Abstract: Common bean is organized into the Middle American and Andean gene pools that arose from a common ancestral population ~100k years ago. Each pool underwent an independent domestication events ~7,000 years ago followed by the subsequent appearance of domesticated races. These independent evolutionary and domesticated events were associated with the appearance of similar phenotypes that were driven by different genetic factors and alleles. This is also the case for the P gene where the E1-I1-E2 deletion is specific to white-seeded race Mesoamerica germplasm that are endemic to southern Mexico and Central America, while the T Deletion is exclusively found in white-seeded race Durango genotypes from northern Mexico. These two mutations, along with the induced mutation of the NEP-2 lineage, though, explain only 62% of the 151 white-seeded Middle American genotypes evaluated. By way of contrast, the white allele of Rc, the P homolog in rice, is found in 98% of all white rice genotypes. A limited analysis did not discover a causative P allele for white-seeded Andean genotypes. That the Middle American mutations described here are not found within the Andean gene pool is not surprising because selection during domestication within each gene pool acted on very few shared genes.