S1A Table Raw phenotypic data for virulence (measured as the amount of necrotic lesion area) and reproduction (pycnidia density within lesion area) on 12 wheat cultivars from 145 <i>Zymoseptoria tritici</i> isolates.

S1B Table: Raw phenotypic data for mean colony area per plate and mean grey value per plate measured in different temperatures and in presence/absence of fungicide from 130 Zymoseptoria tritici isolates. "NA" indicates that no data were obtained due to no colony growth or contamination. S1C Table: Description of 145 Zymoseptoria tritici isolates with their corresponding sampling location, year and NCBI SRR Run ID for the whole genome sequence data used in this study. S1D Table: Number of single nucleotide polymorphisms (SNPs) called on 19 reference genomes at 5% minor allele frequency and 80% genotyping rate for 145 Zymoseptoria tritici isolates. S1E Table: List of phenotypic traits used for GWAS in this study. S1F Table: Number of significant SNP associations above the 5% Bonferroni significance threshold for 20 traits comprising pathogen virulence, reproduction and environmental stress mapped in 19 reference genome SNP datasets. S1G Table: Summary statistics of genome-wide SNPs passing the Bonferroni significance threshold of 5% for specific traits identified 19 reference genome SNP datasets. SNPs are ordered according to the smallest P-value. S1H Table: List of genes with their predicted protein functions in close proximity (< 1 kb) to significant SNPs above the Bonferroni significance threshold (alpha = 0.05) across 19 reference genome SNP datasets for different traits of Zymoseptoria tritici isolates. S1I Table. List of genes with their predicted protein functions in close proximity (< 1 kb) to significant k-mers above the permutation-based significance threshold (5%) for different traits of Zymoseptoria tritici isolates. (XLSX)