Genome-Wide Association Mapping of and Reveals Candidate Genes and New Adjustments to the Host-Pathogen Interaction for Resistance to in Common Bean.

Bean common mosaic necrosis virus (BCMNV) is a major disease in common bean ( L.). Host plant resistance is the primary disease control. We sought to identify candidate genes to better understand the host-pathogen interaction and develop tools for marker-assisted selection (MAS). A genome-wide association study (GWAS) approach using 182 lines from a race Durango Diversity Panel (DDP) challenged by BCMNV isolates NL-8 [Pathogroup (PG)-III] and NL-3 (PG-VI), and genotyped with 1.26 million (SNPs), revealed significant peak regions on chromosomes Pv03 and Pv05, which correspond to and resistance gene loci, respectively. Three candidate genes were identified for NL-3 and NL-8 resistance. Side-by-side receptor-like protein kinases (RLKs), Phvul.003G038700 and Phvul.003G038800 were candidate genes for . These RLKs were orthologous to linked RLKs associated with virus resistance in soybean (). A basic Leucine Zipper (bZIP) transcription factor protein is the candidate gene for . bZIP protein gene Phvul.005G124100 carries a unique non-synonymous mutation at codon 14 in the first exon (Pv05: 36,114,516 bases), resulting in a premature termination codon that causes a nonfunctional protein. SNP markers for and and new markers for and genes were used to genotype the resistance genes underpinning BCMNV phenotypes in the DDP, host group (HG) differentials, and segregating F families. Results revealed major adjustments to the current host-pathogen interaction model: (i) there is only one resistance allele for the locus, and differential expression of the allele is based on presence vs. absence of ; (ii) exhibits dominance and incomplete dominance; (iii) alone confers resistance to NL-8; (iv) was absent from HGs 2, 4, 5, and 7 necessitating a new gene symbol to reflect this change; (v) alone delays susceptible symptoms, and when combined with enhanced resistance to NL-3; and (vi) is on Pv05, not Pv03 as previously thought. These candidate genes, markers, and adjustments to the host-pathogen interaction will facilitate breeding for resistance to BCMNV and related Bean common mosaic virus (BCMV) in common bean.