Quantitative Trait Loci (QTL) Discovery for Resistance to Colletotrichum Crown Rot in Strawberry (Fragaria × ananassa)

Colletotrichum crown rot (CCR) caused by the fungus Colletotrichum gloeosporioides is an important disease in central Florida and throughout the southeastern U.S. We previously identified several highly CCR-resistant accessions in the University of Florida breeding germplasm and found the potential for 74% gain in resistance to this disease in one generation. In order to discover QTLs for CCR resistance, a complex multi-family population consisting of 62 full-sib families from crosses made among 24 parents was evaluated in inoculated field trials during the 2013-14 season. Using whole-genome SNP genotyping and pedigree-based marker-trait association analysis, we found two QTLs in the octoploid strawberry, on LG 6B (Cg1) and LG 5C (Cg2), with the former accounting for 27% of the phenotypic variance. To confirm and more precisely locate the large-effect QTL, Cg1, a validation population consisting of five bi-parental crosses predicted to segregate for resistance at Cg1 was evaluated during the 2015-16 season. The QTL analysis found Cg1 and Cg2 to explain approximately 18% and 11% of the variation, respectively. An in-house developed SNP linkage map representing 38 linkage groups and nearly 6,000 SNP markers were utilized alongside in a pedigree-based genome-wide QTL analysis using FlexQTL™ software. Marker haplotypes and diplotypes for the Cg1 locus were manually constructed for parents and seedlings and confirmed with PediHaplotyper software. We are working to develop high-throughput markers tightly linked to Cg1 to facilitate marker-assisted seedling selection for resistance to CCR at the University of Florida.