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

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 Phytophthora cactorum 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. Supplemental File S1: 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. Supplemental File S2: Phenotypic data for 475 individuals collected across eight timepoints in two years of evaluation. Supplemental File S3: 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. Supplemental File S4: Chromosome IDs and physical addresses for 850K and 50K AxiomTM 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. Supplemental File S5: Genome-wide association study (GWAS) statistics. Supplemental File S6: Phytophthora crown rot (PhCR) resistance phenotypes observed in previous studies (cited in our paper). Supplemental File S7: Physical addresses for annotated genes and 50K AxiomTM 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. Supplemental Table S1: 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.