Pc1: A Large-Effect QTL Conferring Resistance to Phytophthora cactorum in Strawberry

Developing strawberry cultivars with both disease resistance and desirable fruit quality is the major objective of the USDA-NIFA-SCRI-funded RosBREED project and of the University of Florida strawberry breeding program. Plant collapse and resultant yield loss from crown and root rots caused by Phytophthora cactorum cause economic losses in Florida each season. Inoculated field trials were conducted in two consecutive years using clonally replicated seedlings from a circular diallel mating design, representing 122 full-sib families and more than 1,000 seedlings from the UF breeding germplasm. Wide variation was observed in area under the disease progress curve values from 0 to 132. Pedigree-based QTL analysis was performed using 3.8K genetically mapped SNP markers using FlexQTL™ software. One large-effect QTL was detected on LG7D, Pc1, in each of two years. Genome wide association analysis also indicated highly significant markers at the Pc1 locus in both years. The location of the Pc1 region was validated using three different genetic maps. Haploblocks were constructed to examine recombination patterns on LG7D, and SNP haplotypes were constructed in the QTL peak region. Haplotype effects were validated in a set of advanced breeding selections totaling more than 600 individuals. Putative functional allele combinations were constructed by assigning haplotypes to alleles based on their average effects in the validation set. The assigned allele combinations accounted for approximately 40% of the phenotypic variation for resistance/susceptibility in the validation set and strongly indicated partial dominance for the resistant allele(s). This information will help enrich breeding germplasm with the resistant allele.