DOI: 10.25338/b86d3m
title: Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry

description: 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.
description: This data submission contains phenotypic data and genotypic data
 used for Jiménez et al. (2022) "Harnessing Underutilized Gene Bank
 Diversity and Genomic Prediction of Cross Usefulness to Enhance Resistance
 to <em>Phytophthora cactorum</em> in Strawberry". Below
 is a summary of what each file contains. All .xlsx supplementals contain a
 separate worksheet (titled 'READ ME') with more detailed
 information, including a listing of column headers and a description of
 the contents of each column. 
 <strong>Supplemental File S1:</strong> Phytophthora crown rot
 (PhCR) resistance phenotypes (estimated marginal means for resistance
 score and area under the disease progression stairs), AX-184109190
 single-nucleotide polymorphism (SNP) marker genotypes, and associated
 passport data for individuals screened for resistance to PhCR.
 <strong>Supplemental File S2: </strong>Phenotypic
 data for 475 individuals collected across eight timepoints in two years of
 evaluation. <strong>Supplemental File
 S3:</strong> Genotypic data for 40,334 single-nucleotide
 polymorphisms (SNPs) x n= 437 individuals evaluated for Phytophthora crown
 rot (PhCR) resistance phenotypes in this experiment. Genotypes are coded
 as -1, 0, 1, equivalent to AA, AB, and BB. 
 <strong>Supplemental File S4:</strong> Chromosome IDs and
 physical addresses for 850K and 50K Axiom<sup>TM</sup> array
 single-nucleotide polymorphisms (SNPs) in the Camarosa (FaCA1) and Royal
 Royce (FaRR1) genomes are documented and cross-referenced using the
 chromosome nomenclature described by Hardigan et al., 2020.
 <strong>Supplemental File S5:</strong> Genome-wide
 association study (GWAS) statistics. 
 <strong>Supplemental File S6:</strong> Phytophthora crown rot
 (PhCR) resistance phenotypes observed in previous studies (cited in our
 paper). <strong>Supplemental File
 S7:</strong> Physical addresses for annotated genes and 50K
 Axiom<sup>TM</sup> array single-nucleotide polymorphisms
 (SNPs) found in the Mb 21.73-22.99 window on chromosome 7B harboring the
 RPc2 locus. The data rows for candidate genes are highlighted in
 blue. <strong>Supplemental Table
 S1:</strong> Genotype and allele frequencies for the RPc2-associated
 single-nucleotide polymorphism (SNP) marker AX-184109190 among University
 of California (UCD) and non-UCD individuals in the genomic prediction
 training population.