The development of strawberry (Fragaria × 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.
Holistic assessment of fruit quality is an essential component of producing Strawberry varieties that will succeed in the marketplace and improve consumer satisfaction. However, several key quantitative traits are notoriously slow and expensive to assess using standard procedures, namely acidity and aroma, which require titration and gas chromatography and mass spectroscopy compared to others: brix, anthocyanins, and vitamin C, which are measured by refractometer and parallelized plate reader assays. Scaling up evaluations for acidity and aroma has been difficult as the techniques require 5 and 40 mins/sample, respectively, and sample preparation is equally intense, requiring multiple trained hands working for 10-hour sessions to create the sample series for 100 entries. We evaluated the ability (R 2 , RMSE) of a handheld near infrared (NIR) spectrometer, measuring 125 wavelengths between 800 and 1600 nm, and an electronic nose, measuring the reaction of 32 electrochemical sensors that respond to various compounds in gas samples, on 4,000 diverse strawberry accessions to determine if the 5 and 40 min/sample assays can be replaced with a 1 (0.33%) sec/sample (NIR) and 2 (5%) min/sample (E-nose) assay that require no additional sample prep. We also assess the NIR's ability to predict brix, anthocyanins, and vitamin C. With these two sensors, we will be able to increase the scale of early generation evaluation from hundreds to thousands of samples in early generations, produce full datasets prior to deadlines in the breeding program, and make more reliable genetic gains for quality traits affecting marketability and consumer acceptance.