Snap bean (Phaseolus vulgaris L.) is an important crop to diversified vegetable production in the Great Lakes Region of the United States, but an aphid-transmitted virus disease complex threatens sustainable production. The component viruses include the potyviruses Clover yellow vein virus (ClYVV) and Bean yellow mosaic virus (BYMV) that are acquired and transmitted rapidly by dispersing aphid vectors. This situation necessitates the identification, introgression, and deployment of plant virus resistance alleles to achieve effective and ecologically sensitive control. Genetic variation for resistance to ClYVV was characterized at the phenotypic and molecular genetic levels. The relationship of three previously putative independent resistance alleles, cyv, desc, and bc-3 was resolved into an allelic series at the Bc-3 locus where the strain and species-specific resistance spectrum was allele specific. Given previous advances, this pathosystem presented an immediate candidate gene, P. vulgaris eIF4E (PveIF4E), as the molecular basis for resistance. A complete association between specific non-synonymous single nucleotide polymorphisms (SNPs) and virus resistance led to the identification of the putative molecular determinants for resistance to ClYVV and Bean common mosaic necrosis virus (BCMNV) strain NL 3 D. PveIF4E allele specific assays were developed for rapid introgression of bc-3 and the novel bc-32 allele into bean breeding programs. Phenotypic evaluation and the allele specific assays were used to further characterize ClYVV resistance in a large and representative sample of common bean genetic diversity. The result was the identification of novel ClYVV resistance in all major market classes, and the validation of the use of the assays for allele mining in germplasm collections. These efforts also lead to the phenotypic identification of ClYVV resistance alleles at independent loci, and established a model for resistance that now includes By-2 and the bc-u, bc-22 combination. The novel and highly efficient genotyping-by-sequencing (GBS) method was adapted to common bean and used to map the position of the By-2 allele for resistance to BYMV and ClYVV. By-2 was mapped to within a 974k kb region on the distal portion of chromosome 2. This effort generated genomic resources for fine mapping and assays that were also validated for marker-assisted selection.