Genotyping-by-Sequencing Enabled Mapping and Marker Development for the By-2 Potyvirus Resistance Allele in Common Bean

Since its emergence in 2001, an aphid-transmitted virus disease complex has caused substantial economic losses to snap bean (Phaseolus vulgaris L.) production and processing in the Great Lakes Region of the United States. The general ineffectiveness of chemical control measures for nonpersistently transmitted viruses established an urgent need for the development and deployment of cultivars with resistance to the component viruses. Our objectives were to further characterize the inheritance of resistance to Bean yellow mosaic virus (BYMV), which is conditioned by the By-2 allele, to adapt genotyping-by-sequencing (GBS) to common bean to discover and genotype genome-wide single nucleotide polymorphisms (SNPs) in a set of recombinant inbred lines (RILs) derived from an introgression program, and to enable and validate marker-assisted selection for By-2. We optimized ApeKI for GBS in common bean and retained 7530 high-quality SNPs that segregated in our introgression RILs. A case-control genome-wide association study (GWAS) was used to discover 44 GBS SNPs that were strongly associated with the resistance phenotype and which delimited a 974 kb physical interval on the distal portion of chromosome 2. Seven of these SNPs were converted to single-marker Kompetitive Allele-Specific Polymerase chain reaction (KASP) assays and were demonstrated to be tightly linked to BYMV resistance in an F-2 population of 185 individuals. This research enables marker-assisted selection of By-2, provides enhanced resolution for fine mapping, and demonstrates the potential of GBS as a highly efficient, high-throughput genotyping platform for common bean breeding and genetics.