Fine mapping of the unique Ur-11 gene conferring broad resistance to the rust pathogen of common bean

Authors: VALENTINI, GISELI - North Dakota State University; HURTADO-GONZALES, OSCAR - Animal And Plant Health Inspection Service (APHIS); XAVIER, LARRISA - Oak Ridge Institute For Science And Education (ORISE); He, Ruifeng; GILL, UPINDER - North Dakota State University; Song, Qijian; PASTOR CORRALES, MARCIAL - Retired ARS Employee

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2025
Publication Date: 3/4/2025
Citation: Valentini, G., Hurtado-Gonzales, O., Xavier, L., He, R., Gill, U., Song, Q., Pastor Corrales, M. 2025. Fine mapping of the unique Ur-11 gene conferring broad resistance to the rust pathogen of common bean. Theoretical and Applied Genetics. 138. Article e64. https://doi.org/10.1007/s00122-025-04856-5.
DOI: https://doi.org/10.1007/s00122-025-04856-5

Interpretive Summary: Common bean rust is one of the most serious diseases threatening the production of beans, a major source of food and essential nutrients worldwide. Development of new bean varieties with resistance genes has proven to be the most effective way to overcome multiple virulent strains of rust pathogens. Previous studies have shown that a gene called Ur-11 confers broad-spectrum resistance to different strains, but it has not yet been possible to finely map the gene in the genome. We finely mapped the common bean rust resistance gene Ur-11 to a narrow physical interval of 9 kb containing only a single candidate gene (PHAVU_011G200900g) with functions related to pathogen resistance by phenotyping, genotyping, and whole-genome sequencing. Furthermore, we developed highly specific and accurate molecular markers that are almost perfectly associated with this gene in a large number of common bean germplasms and breeding lines, which can be used for the selection and breeding of rust-resistant varieties. This information will also help in subsequent cloning of the resistance gene and understanding of the mechanisms behind resistance.

Technical Abstract: The extensive virulence diversity of Uromyces appendiculatus threatens common bean (Phaseolus vulgaris) production. The Ur-11 gene present in the Guatemalan black bean PI 181996 confers resistance to 89 of 90 virulent races of U. appendiculatus. We describe here the fine-mapping of Ur-11 and the development and validation of a DNA marker tightly linked to Ur-11. The inheritance of resistance study included the inoculation of an F2 population from the cross between the susceptible Pinto 114 with the resistant PI 181996 with four races of U. appendiculatus. This study established that the rust resistance in PI 181996 was conferred by Ur-11. We then fine mapped Ur-11 using F2 plants and F2:3 families, high-throughput SNP genotyping, SSRs and KASPs marker development, whole genome sequencing, and local haplotype analysis. Ur-11 was positioned in a 9.01Kb genomic region on chromosome Pv11 flanked by KASP markers SS375 and SS322. This genomic region included a candidate gene encoding a nucleotide-binding site and leucine rich-repeat domain with pathogen resistance functions. The validation of the KASP markers was performed on a panel of 206 diverse common bean cultivars that were inoculated with four races. The SS322 KASP marker was 97.5% accurate in predicting the presence of Ur-11 in common bean plants. These results suggest that S322 will be highly useful for the development of cultivars combining Ur-11 with other rust resistance genes that would provide broad and durable resistance to the hyper virulent bean rust pathogen.