Genome-wide association mapping of bc-1 and bc-u reveals candidate genes and new adjustments to the host-pathogen interaction for resistance to Bean common mosaic necrosis virus in common bean

Authors: SOLER-GARZON, ALVARO - Washington State University Extension Service; MCCLEAN, PHIL - North Dakota State University; Miklas, Phillip - Phil

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/21/2021
Publication Date: 6/29/2021
Citation: Soler-Garzon, A., McClean, P., Miklas, P.N. 2021. Genome-wide association mapping of bc-1 and bc-u reveals candidate genes and new adjustments to the host-pathogen interaction for resistance to Bean common mosaic necrosis virus in common bean. Frontiers in Plant Science. 12. Article 699569. https://doi.org/10.3389/fpls.2021.699569.
DOI: https://doi.org/10.3389/fpls.2021.699569

Interpretive Summary: Bean common mosaic necrosis virus (BCMNV) is the most problematic virus infecting common bean worldwide. It is a global pathogen problem because the virus is seed-borne. There is zero tolerance for the virus in seed production in the western U.S. The best control is via deployment of resistance genes in the common bean host. We mapped and tagged two genes bc-u and bc-1 effective against BCMNV. The markers were used in segregating populations to reveal significant adjustments to the host-pathogen interaction model. These adjustments to the model direct breeders worldwide to deploy bc-u in combination with other genes to broaden and enhance the stability of resistance to BCMNV. Markers linked with these genes will help breeders deploy them via marker-assisted selection.

Technical Abstract: Bean common mosaic necrosis virus (BCMNV) is a major disease in common bean (Phaseolus vulgaris 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. A GWAS approach using a panel of 182 lines from race Durango (DDP) challenged by BCMNV isolates NL-8 (Pathogroup-III) and NL-3 (Pathogroup-VI), and genotyped with 1.26 million SNPs, revealed significant peak regions on chromosomes Pv03 and Pv05, which correspond to bc-1 and bc-u resistance gene loci, respectively. Side-by-side receptor-like protein kinases (RLKs), Phvul.003G038700 and Phvul.003G038800, were candidate genes for bc-1. These RLKs were orthologous to linked RLKs associated with virus resistance in soybean (Glycine max). A basic Leucine Zipper (bZIP) transcription factor protein is the candidate gene for bc-u. 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 bc-1 and bc-u, and new markers for I and bc-3 genes were used to genotype the resistance genes underpinning BCMNV phenotypes in the DDP, host group differentials, and segregating F3 families. Results revealed major adjustments to the current host-pathogen interaction model: i) there is only one resistance allele bc-1 for the Bc-1 locus, and differential expression of the allele is based on presence versus absence of bc-u; ii) bc-1 exhibits dominance and incomplete dominance; iii) bc-1 alone confers resistance to NL-8; iv) bc-u was absent from host groups 2, 4, 5, and 7 necessitating a new gene symbol bc-ud to reflect this change; v) bc-ud alone delays susceptible symptoms, and when combined with bc-1 enhanced resistance to NL-3; and vi) bc-ud 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.