Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry

The development of strawberry Fragaria x ananassa cultivars resistant to
Phytophthora crown rot (PhCR), a devastating disease caused by the
soil-borne pathogen Phytophthora cactorum, has been challenging, partly
because resistance phenotypes are quantitative and only moderately
heritable. To develop deeper insights into the genetics of resistance and
build the foundation for applying genomic selection, a genetically diverse
training population was screened for resistance to California isolates of
the pathogen. Here we show that genetic gains in breeding for resistance
to PhCR have been negligible (3% of the cultivars tested were highly
resistant and none surpassed early twentieth-century cultivars).
Narrow-sense heritability for PhCR resistance ranged from 0.35-0.57. Using
multivariate GWAS, we identified a large-effect locus (predicted to be
RPc2) that appears to be ubiquitous, slowed symptom development, explained
43.6-51.6% of the genetic variance, was necessary but not sufficient for
resistance, and was strongly associated with calcium channel and other
genes with known plant defense functions. The addition of underutilized
gene bank resources to our training population doubled additive genetic
variance, increased the accuracy of genomic selection, and enabled the
discovery of individuals carrying favorable alleles that are either rare
or not present in modern cultivars. The incorporation of an
RPc2-associated SNP as a fixed effect increased genomic prediction
accuracy from 0.40 to 0.55. Finally, we show that parent selection using
genomic-estimated breeding values, genetic variances, and cross-usefulness
holds promise for enhancing resistance to PhCR in strawberry.