Genome-wide prediction of powdery mildew resistance in the octoploid strawberry

Powdery mildew (PM) caused by Podosphaera aphanis is a major fungal disease in cultivated strawberry. Characterization of resistance loci has been challenging for breeders and geneticists due to the complex and polygenic nature of resistance. Genome-wide prediction (GWP) utilizes genome-wide markers to predict the performance of individuals and accelerate genetic gains for polygenic traits. In the present study, we implemented GWP models using six pedigree-connected full-sib families from crosses among four University of Florida advanced selections. These families were evaluated in a replicated field trial, and 250 to 9,000 polymorphic single nucleotide polymorphism (SNP) markers were chosen based on genome coverage and polymorphism. Half-sibs were used as a training population to rank seedlings within each cross (full-sib family). The highest predictive abilities using Bayes B, GBLUP and RKHS methods were 0.36, 0.38 and 0.38, respectively. The three methods had comparable parent selection efficiencies, and within-family genetic gains were at least 10% over the family mean when selecting the top 10% of seedlings ranked by GWP. As few as 500 SNP markers were sufficient to achieve comparable results. Overall, this study demonstrates the potential for application of within-family GWP for rapid genetic improvement of powdery mildew resistance in strawberry seedling families.