Fig. 2
Genome-wide association mapping for virulence. Manhattan plots showing SNP marker association p-values for (a) pycnidia count and (b) ρleaf (pycnidia count per cm2 of leaf area). The genome-wide association mapping analyses was performed based on a mixed linear model including a kinship matrix. The blue and red lines indicate the significance thresholds for Bonferroni (⍺ = 0.05) and false discovery rate (FDR) at 5%, respectively. The dotted line represents the most significant association on chromosome 1 (snp_chr1_4521202). c Boxplot showing the pycnidia counts of isolates carrying the reference allele G or alternative allele T at the top significant SNP. d Zoomed in Manhattan plot for association p-values of SNPs in a ~ 25 kb region centered on the top SNP snp_chr1_4521202. Horizontal lines represent the Bonferroni threshold (⍺ = 0.05). e Genotyping rates of SNPs in the mapping population. f Linkage disequilibrium r2 heatmap of the entire region. Linkage disequilibrium decay plot focused on the most significantly associated SNP with nearby SNPs. g-h Correlation plot of pycnidia count with gene expression of the flanking effector candidate gene (Zt09_1_01590) and the serine-type endopeptidase gene (Zt09_1_01591). I-J) Transcriptional profiling of the effector gene and the serine-type endopeptidase gene on wheat 7, 12, 14, and 28 days post infection