Pedigree-based QTL Detection for Disease Resistance and Fruit Quality Traits: An Overview of the University of Florida Strawberry Breeding Program

The University of Florida (UF) strawberry breeding program develops cultivars for the Florida industry, the second largest producer of fresh strawberries in the United States. There is a need for new strawberry cultivars with both improved disease resistance and superior fruit quality. This need is being addressed through the USDA-NIFA-SCRI project entitled “RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars.” The creation of the Affymetrix IStraw90^® Axiom^® SNP array revolutionized genetic research in octoploid strawberry. A dataset of 3,624 genetically mapped SNP markers spanning 28 linkage groups was obtained for 795 pedigree-connected individuals in the UF strawberry breeding population. Phenotypic data from one year of inoculated field trials for three disease resistance traits and non-inoculated trials for four fruit quality traits were obtained and analyzed using FlexQTL™ software. A single major locus controlling resistance to Xanthomonas fragariae (causal agent of angular leaf spot) was discovered on linkage group (LG) 6D explaining ~96% of phenotypic variation (PVE) and Bayes Factor (BF) >10 (BF 0–2 = nonsignificant; 2–5 = positive; 5–10 = strong; > 10 = decisive evidence). Large-effect quantitative trait loci (QTL) were also discovered for resistance to Phytophthora cactorum (causal agent of Phytophthora crown rot) on LGs 7D (BF=29) and 4B (BF=28) together accounting for 48% PVE and for Colletotrichum gloeosporioides (causal agent of Colletotrichum crown rot) on LGs 6B (BF=29) and 5C (BF=5) with 39% PVE. For the fruit quality traits, QTL for soluble solids content were detected on LGs 1A (BF=8), 3A (BF=9), 5B (BF=6) with 41% PVE; for average fruit weight on 4B (BF=6) and 6C (BF=16) with 36% PVE; for fruit number on LGs 1C (BF=6), 3D (BF=9), 5C (BF=6) and 6D (BF=6) with 31% PVE; and for total culled fruit on LGs 1B (BF=8), 2A (BF=5) and 3D (BF=29) with 54% PVE. In general disease traits appear to be conferred by 1–2 major loci while most of the fruit quality traits appear to be controlled by a larger number of small-effect QTL, with an occasional large-effect QTL. QTL-allele mining is underway for these regions, and a second year of phenotypic data on new individuals is being collected for QTL validation. Ultimately, high-throughput DNA-based markers will be developed for major loci for use in marker-assisted breeding applications. RosBREED is funded by the USDA-NIFA-SCRI Award number 2014-51181-22378.