Dataset containing the supplementary material in support of the PhD thesis "Investigating durable resistance to Phytophthora cactorum in strawberry and apple". These include the details of individual genotypes, linkage maps, markers and QTL loci used and resulted from mapping experiments. They also include details of the RNA sequencing results from various experiments including sequencing and alignment quality, and differential expression analysis results. Also included are the results of gene set enrichment analysis performed on differentially expressed gene sets.