QTL Detection and Allele Mining for Phytophthora cactorum Resistance in University of Florida Strawberry Breeding Germplasm

Developing strawberry cultivars with both disease resistance and desirable fruit quality is a challenging but important objective of the RosBREED consortium and of the University of Florida strawberry breeding program. Plant collapse and resultant yield loss from Phytophthora crown rot caused by Phytophthora cactorum results in economic losses in Florida each season. An inoculated field trial was conducted during the 2013–14 season using clonally replicated seedlings from a circular diallel mating design, representing 62 full-sib families and 566 progeny from the elite breeding population. Plant mortality was recorded weekly and the area under the disease progress curve (AUDPC) was calculated for each individual. A wide variation from 0 to 132 was observed in AUDPC scores. Pedigree-based QTL analysis was performed using 3,624 genetically mapped SNP markers spanning 28 linkage groups (LG) using FlexQTL™ software. Three large-effect QTL were detected, one on LG 4B, Pc1 (Bayes Factor = 28), and two others on LG 7D, Pc2 (BF = 15) and Pc3 (BF = 14), together accounting for ~ 48% of phenotypic variation. Breeding values and genotype probabilities associated with each individual associated with the three loci were used to predict allele effects of the segregating QTL. Most of the families were segregating for Pc2 and Pc3, but very few for Pc1. Individuals inheriting pc | pc alleles (pc = associated with low mortality; Pc = associated with high mortality) at all the three loci (pc1pc1 | pc2pc2 | pc3pc3) were associated with low AUDPC scores ranging from 0 to 37. As the proportion of the Pc allele at any of the three loci increased, mortality also increased. Interestingly, none of the individuals were homozygous for susceptible allele at Pc1. The presence of a single Pc allele at Pc1 was consistently associated with plant mortality very early in the season, resulting in AUDPC scores ranging from 84 to 132. Other allelic combinations that fell in this range were either Pc1pc1 | Pc2Pc2 | Pc3Pc3 or Pc1pc1 | Pc2pc2 | Pc3Pc3 or Pc1pc1 | pc2pc2 | Pc3Pc3 indicating stronger effect of Pc1 & Pc3 than Pc2. Because of the complex pedigree structure, it may be possible that more than two alleles may be segregating at each of the loci. Haplotype analyses for the three loci are underway toward validation of allele effects in a separate set of populations. RosBREED is funded by the USDA-NIFA-SCRI Award number 2014-51181-22378.