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 (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 single-nucleotide polymorphisms (SNPs), revealed significant peak regions on chromosomes Pv03 and Pv05, which correspond to bc-1 and bc-u 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 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 (HG) 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 vs. 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 HGs 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.
Highlights
Bean common mosaic necrosis virus (BCMNV) and Bean common mosaic virus (BCMV) are related positive-stranded RNA viruses in the Potyvirus genus that infect common bean (Phaseolus vulgaris L.) worldwide
A total of 182 Durango Diversity Panel (DDP) lines were evaluated for reaction to BCMNV strains NL-3 (PG-VI) and NL-8 (PG-III) under greenhouse conditions
The DDP lines could be separated into two major groups based on M, dM, and mild mosaic (mM) vs. TN, vein necrosis (VN), VN+, and NLL symptoms indicating absence (96 lines) and presence of the dominant I gene (61 lines), respectively (Table 2; Supplementary Table S5)
Summary
Bean common mosaic necrosis virus (BCMNV) and Bean common mosaic virus (BCMV) are related positive-stranded RNA viruses in the Potyvirus genus that infect common bean (Phaseolus vulgaris L.) worldwide. Seed-borne transmission plagues subsistence farmers and other growers who rely on planting their own “bin-run” seed. These viruses can cause greater than 80% yield loss in common bean production fields (Morales, 2003). Resistance to BCMNV and BCMV in the common bean is regulated by the dominant I gene and six recessive alleles (bc-1, bc-12, bc-2, bc-22, bc-3, and bc-u) distributed across four loci (Drijfhout, 1978). Strain diversity is classified into eight pathogroups (PG) based on interactions with 12 host group (HG) differential cultivars possessing different resistance gene combinations, PG I to VII referenced in Drijfhout et al (1978) and PG VIII identified by Feng et al (2015)
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