What Have We Learned during Marker-locus Trait Validation for Rpf1 Red Stele Resistance in Strawberry?

Red stele (Phytophthora fragariae Hickman var. fragariae) is a devastating root rot disease in strawberries (Fragaria L.). Several sources for genetic resistance are exploited in breeding and several race-specific R-genes are known. Recently, a tightly linked SSR marker was found for the Rpf1 gene at Wageningen-UR, The Netherlands. As part of the “RosBREED: Enabling Marker-Assisted Breeding in Rosaceae” project, 947 strawberry individuals were chosen to represent the breadth of relevant diversity used in breeding the domesticated strawberry. A simple sequence repeat (SSR) set composed of the Rpf1 SSR marker and ARSFL007 was used to genotype the RosBREED strawberry germplasm for presence of the Rpf1 marker and for parentage confirmation. One hundred and fifty three (153) of the RosBREED individuals with known and unknown responses to the red stele pathogen were inoculated in bench tests to two races of this disease to validate this marker-Rpf1 association. The Microsatellite Allele Dose and Configuration Establishment (MADCE) technique was used to establish the allelic composition of three subgenomes in the Rpf1 SSR and each of the four subgenomes in ARSFL007. Using manual parentage verification followed by FlexQTL-based parentage check in the 947 individuals identified 42 progeny and 11 cultivars that did not segregate according to pedigree. Genotypes for 24 out of 84 parents used in crosses were inferred using FlexQTL and pedigree was corrected. The Rpf1 gene confers resistance to Canadian race 4 (Cdn-4) and is ineffective against Canadian race 5 (Cdn-5). Of the 153 inoculated individuals, 16 individuals, mainly of wild origin were identified as having other factors of resistance by exhibiting resistance to race Cdn-5 and may be valuable for widening the genetic base of resistance in commercial cultivars. To avoid epistatic effects, these individuals were excluded from validation along with 50 other individuals that were not replicated or that had borderline disease scores. For the remaining 87 individuals that showed severe disease scores for Cdn-5, 24 were resistant to Rpf1 and 63 were susceptible to both races. The Rpf1 SSR marker was present in 14 of 24 individuals that were resistant to Rpf1 and absent in 50 of 63 accessions that were susceptible to this disease. Causes for the 79.3% marker-trait association are being investigated and will be discussed.