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.本数据集提交内容包含用于Jiménez等人2022年发表的论文《利用未充分利用的基因库多样性与杂交利用价值基因组预测提升草莓对疫霉（Phytophthora cactorum）冠腐病的抗性》的表型数据与基因型数据。下文将逐一说明各文件的具体内容。所有.xlsx格式的补充文件均包含名为"READ ME"的独立工作表，其中收录了更为详尽的信息，包括列标题清单与各列内容的详细说明。 补充文件S1：包含疫霉冠腐病（Phytophthora crown rot, PhCR）抗性表型数据（抗性评分与病害进展阶梯下面积的估计边际均值）、AX-184109190单核苷酸多态性（single-nucleotide polymorphism, SNP）标记基因型，以及针对PhCR抗性进行筛选的试验材料的相关种质护照数据。 补充文件S2：包含475份试验材料在两年评估周期内8个时间点采集的表型数据。 补充文件S3：包含针对本实验中PhCR抗性表型进行评估的437份试验材料与40334个单核苷酸多态性（SNPs）的基因型数据。基因型以-1、0、1分别编码为AA、AB与BB。 补充文件S4：记录了Camarosa（FaCA1）与Royal Royce（FaRR1）基因组中，850K与50K Axiom™阵列的单核苷酸多态性（SNPs）的染色体ID与物理位置，并依据Hardigan等人2020年提出的染色体命名规则进行交叉参照。 补充文件S5：包含全基因组关联研究（genome-wide association study, GWAS）统计数据。 补充文件S6：包含既往研究中报道的疫霉冠腐病（PhCR）抗性表型数据（本论文已引用该类研究）。 补充文件S7：包含7B染色体上RPc2位点所在的21.73-22.99 Mb区间内的注释基因与50K Axiom™阵列单核苷酸多态性（SNPs）的物理位置，候选基因的数据行以蓝色高亮标注。 补充表S1：包含基因组预测训练群体中，加州大学（University of California, UCD）与非UCD试验材料内与RPc2相关的单核苷酸多态性（SNP）标记AX-184109190的基因型与等位基因频率。