Integrative genomic analyses reveal candidate genes for the Ur-3 and Ur-7 rust resistance loci in common bean

Authors: SOLER-GARZON, ALVARO - Washington State University; VALENTINI, GISELI - Montana State University; PASTOR-CORRALES, MARCIAL - Retired ARS Employee; He, Ruifeng; Miklas, Phillip

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/21/2026
Publication Date: 5/26/2026
Citation: Soler-Garzon, A., Valentini, G., Pastor-Corrales, M., He, R., Miklas, P.N. 2026. Integrative genomic analyses reveal candidate genes for the Ur-3 and Ur-7 rust resistance loci in common bean. The Plant Genome. 19(2). Article e70253. https://doi.org/10.1002/tpg2.70253.
DOI: https://doi.org/10.1002/tpg2.70253

Interpretive Summary: Bean rust is a damaging disease that can reduce common bean yields under warm, humid conditions. Because the rust pathogen changes rapidly, chemical control is often unreliable, making genetic resistance the most effective management strategy. This study examined two widely used rust resistance genes, Ur-3 and Ur-7, using advanced DNA sequencing. Researchers identified the genes responsible for resistance and developed reliable DNA markers to track them. The results explain past breeding challenges with Ur-3 and show that Ur-7 is genetically stable. These new markers allow breeders to quickly select rust-resistant plants without field screening, speeding variety development and improving resistance durability for growers.

Technical Abstract: Bean rust, caused by Uromyces appendiculatus, severely limits the productivity of common bean (Phaseolus vulgaris L.), an essential source of protein and micronutrients in human diets worldwide. Durable disease management relies primarily on host resistance; however, the molecular architecture of several key rust resistance loci remain unresolved. We sought to characterize the genomic structure of the Ur-3 and Ur-7 loci and developed associated molecular markers. An integrative genomic framework combining high-resolution long-read genome assemblies, recombinant inbred line populations, and single-nucleotide polymorphism–based and k-mer–based genome-wide association studies was used to fine-map both loci. Extensive structural variation was revealed for the Ur-3 locus at the distal end of chromosome Pv11, whereas Ur-7 localized to a low-recombination pericentromeric region of the same chromosome. A coiled-coil nucleotide-binding leucine-rich repeat gene embedded within an NB-ARC–rich cluster was identified as the most likely candidate underlying Ur-3 (Pv11: 50,205,868 – 50,209,452 bases; USDA Rattler reference). In contrast, the refined Ur-7 interval contained a Toll/interleukin-1 receptor NLR gene as the leading candidate (Pv11: 36,604,755 - 36,611,252; UI 111 reference). Gene-based markers developed from these candidates showed complete correspondence with rust phenotypes. Marker-assisted selection (MAS) for Ur-3 and Ur-7 will contribute to the development of durable rust resistance against the highly variable bean rust pathogen U. appendiculatus.