Genetic mapping resistance to white mold in two pinto bean recombinant inbred line populations

Authors: SOLER-GARZON, ALVARO - Washington State University; LOPES,SUZA, FERNANDA - Universidade Federal De Lavras; ROY, JAYANTA - North Dakota State University; CLEVENGER, JOSH - Hudsonalpha Institute For Biotechnology; MYERS, ZACHARY - Hudsonalpha Institute For Biotechnology; KORANI, WALID - Hudsonalpha Institute For Biotechnology; Song, Qijian; Porch, Timothy - Tim; MCCLEAN, PHILLIP - North Dakota State University; Miklas, Phillip - Phil

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/3/2024
Publication Date: 12/9/2024
Citation: Soler-Garzon, A., Lopes,Suza, F., Roy, J., Clevenger, J., Myers, Z., Korani, W., Song, Q., Porch, T.G., Mcclean, P., Miklas, P.N. 2024. Genetic mapping resistance to white mold in two pinto bean recombinant inbred line populations. The Plant Genome. Article e20538. https://doi.org/10.1002/tpg2.20538.
DOI: https://doi.org/10.1002/tpg2.20538

Interpretive Summary: White mold significantly affects bean yields, causing significant yield losses of 30 to 100% under environmental conditions favorable to the pathogen. Certain common beans in the Mesoamerican gene pool, such as pinto bean, great northern bean, pink bean, small red bean, etc., are highly susceptible to this disease. In the past, pinto beans resistant to white mold were bred using resistance sources from non-pinto beans, but due to the different genetic background of the resistance sources and their adverse effects on agronomic traits, breeding pinto bean lines with acceptable agronomic traits could not be recovered. In this study, we identified and validated several genomic regions regulating white mold resistance from two pinto bean accessions, USPT-WM-12 and VCP-13, which are highly resistant to white mold, and characterized candidate genes controlling the resistance. This information will help introduce resistance from the two resistance sources to improve white mold resistance in pinto beans.

Technical Abstract: White mold, caused by the fungus Sclerotinia sclerotiorum, is a devastating disease affecting common bean production worldwide. Breeding for resistance to white mold is challenging due to the quantitative nature of resistance and the complexity of the genetic mechanisms. This research aimed to validate and characterize physiological resistance using greenhouse straw tests under controlled conditions and field resistance under natural environments in the pinto dry bean market class. Classical QTL mapping and Khufu de novo QTL-seq were employed to detect and narrow QTL intervals and identify candidate genes associated with white mold resistance in two pinto bean recombinant inbred line (RIL) populations, PT9-5-6/USPT-WM-12 (P2) and PT12-37/VCP-13 (P3). Eleven QTL related to white mold resistance were identified: five QTL in P2 and six in P3. New QTL including WM1.4 (Pv01: 55.7 – 57.0 Mb) in P2, and WM1.5 (Pv01: 57.4 – 58.6 Mb) and WM7.7 (Pv07: 41.6 – 42.7 Mb) in P3 were discovered. Existing major-effect QTL were validated: WM5.4 (34% - phenotypic variation explained) and WM7.4 (20%) in straw tests, and WM2.2 (15%) and WM3.1 (27%) in field conditions. QTL for avoidance traits such as resistance to lodging, late maturity, or estimated seed yield overlapped WM2.2 in P2, and WM1.5, WM3.1, WM5.4, and WM7.7 in P3. Two QTL, WM5.4 (Pv05: 7.0 – 38.7 Mb) and WM8.1 (Pv08: 0.8 – 3.0 Mb) were associated with Phaseolus coccineus genome introgressions in the resistant parent VCP-13. These QTL conditioning resistance to white mold in pinto bean backgrounds provide narrowed genomic intervals and putative candidate genes as marker-assisted selection targets for white mold resistance improvement in pinto bean.