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

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 remains unresolved. We sought to characterize the genomic structure of the Ur-3 and Ur-7 loci and develop 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 for Ur-3 and Ur-7 will contribute to the development of durable rust resistance against the highly variable bean rust pathogen U. appendiculatus.