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

Key message: Fine mapping positioned the Ur-11 rust resistance gene in common bean to a narrow 9 kb genomic region and enabled the development of a KASP marker tightly linked to Ur-11 for use in gene pyramiding to achieve durable rust resistance. The extensive virulence diversity of the fungal pathogen Uromyces appendiculatus threatens common bean (Phaseolus vulgaris) production. The Ur-11 gene present in the Guatemalan common bean accession PI 181996 conferred 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. An F₂ population from the cross between the susceptible Pinto 114 with the resistant PI 181996 was inoculated 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 F_2:3 families, high-throughput SNP genotyping, SSRs and KASPs marker development, whole-genome sequencing, and local haplotype analysis. Ur-11 was positioned in a narrow 9.01 Kb genomic region on chromosome Pv11 flanked by KASP markers SS322 and SS375. 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 SS322 KASP marker was performed on a panel of 206 diverse common bean cultivars that were inoculated with four races of U. appendiculatus. The SS322 marker was 97.5% accurate in identifying the presence of Ur-11 in common bean plants. These results suggest that S322 will be a highly effective molecular marker for the development of common bean cultivars with Ur-11 alone and combining Ur-11 with other rust resistance genes that would confer broad and durable resistance to the hypervirulent bean rust pathogen.