QTL mapping of resistance to the Cucumber mosaic virus P1 strain in pepper using a genotyping-by-sequencing analysis

Cucumber mosaic virus (CMV), a member of the Cucumovirus genus in the family Bromoviridae, is a frequently occurring virus in pepper worldwide. A broad host range, which includes many weed species and a large number of insects, means it is difficult to control CMV in the field. CMV resistance has been reported in Capsicum spp. In Korea, the C. annuum ‘Bukang’ cultivar is resistant to the CMV_FNY and CMV_Korean strains; however, a new strain (CMV_P1) is able to infect the resistant cultivars. Therefore, it is necessary to pursue CMV_P1 resistance in pepper breeding. In this study, we surveyed the quantitative trait loci (QTL) for resistance to CMV_P1 using a single-seed-descent (SSD) F₃ segregating population derived from a cross between a resistant line, ‘A1’, and a susceptible line, ‘2602.’ A total of 174 plants were evaluated for resistance to CMV_P1 at 30 days after mechanical inoculation, with phenotypes confirmed by reverse transcription PCR. The number of resistant and susceptible plants was 88 and 86, respectively. Of these, 96 individuals including 48 resistant lines and 48 susceptible lines were used for a genotyping-by-sequencing (GBS) analysis. Approximately 19,000 single-nucleotide polymorphism (SNP) genotypes were obtained. Using the SNP data, a pepper genetic linkage map consisting of 906 SNP markers was constructed. The map showed 12 linkage groups with a total linkage distance of 1,272.9 cM. QTL analysis using a composite interval mapping (CIM) method revealed that two QTLs, cmvP1-5.1 and cmvP1-10.1, located on chromosomes 5 and 10, respectively, had R² (coefficient of determination) values of 17.81% and 22.78%. This information will be helpful for developing SNP markers linked to CMV_P1-resistant QTLs and for developing new CMV_P1-resistant pepper cultivars.