FIGURE 3.

Transcriptome analysis of near-isogenic lines (NILs) with either subQTL DM4.1.2 or DM4.1.3. Analysis of transcriptome data from leaves of three cucumber genotypes (HS279, susceptible, and NILs DM4.1.2 and DM4.1.3, both partially resistant) 3 days post P. cubensis inoculation or mock control, with three independent samples per genotype × treatment combination. (A) Individuals homozygous for partial introgressions corresponding to subQTL DM4.1.1 and DM4.1.2 (NIL DM4.1.1/.2) or DM4.1.3 (NIL DM4.1.3) were selected to develop NILs. Bars represent the allele of genotypes at marker locations on the DM4.1 interval. Black bars indicate the PI 197088 allele and white bars indicate the HS279 allele. (B) Principal component analysis of transcriptome data. (C) MA plots for pairwise differential expression analysis contrasts between mock-treated and P. cubensis inoculated samples. Each point represents a detected gene. The X-axis represents the mean normalized counts per gene under both conditions, whereas the Y-axis represents the log₂ fold change in P. cubensis inoculated samples compared to mock-treated samples. Differentially expressed genes (adjusted p < 0.05) are represented in red. Blue lines represent a twofold change threshold. (D) MA plots for pairwise differential expression analysis contrasts between genotypes under mock-treated (left column) or P. cubensis inoculated (right column) conditions. (E) Venn diagram representing differentially expressed upregulated (in red) and downregulated (in blue) genes in P. cubensis inoculated samples compared to mock-treated samples. Differentially expressed genes are here defined as statistically significant (adjusted p < 0.05) and >2-fold up- or downregulated.