Differential gene expression analysis

The PCA analyses showed marked differences between the gene expression profiles of the genotypes and their responses to the inoculation. Similarly, the genes expressed differentially between mildew inoculated and mock-inoculated plants showed high genotype-specific variation. The R1 genotype had the highest number of differentially expressed (DE) transcripts among all genotypes, 3803, from which about 2000 had absolute log2 fold change greater than one. On the other hand, the S2 genotype had the lowest number of DE transcripts, 43, with only 20 having absolute log2 fold change greater than one (Table 1; Supplementary Table 2).