Figure 6

Tubers of the + RB line have a higher frequency of differentially expressed (DE) genes 48 hours post inoculation (hpi) with Phytophthora infestans, compared to WT (24 and 48 hpi) and +RB at 24 hpi. Tuber samples collected 0, 24, and 48 hpi were subjected to RNA-seq, revealing a total of 1,102 DE genes between water- and P. infestans-inoculated comparisons within the same genotype and the same time. (A) All 1,102 DE genes were analyzed using the “Venn count” function in the limma packages of R [53] and results were summarized as a Venn diagram. Red: WT 24 hpi; yellow: +RB 24 hpi; blue: WT 48 hpi; green: +RB 48 hpi. The results show that the +RB line is the main contributor of DE genes during water- vs. P. infestans-inoculated comparisons. (B) All 1,102 DE genes were also assigned to a MapMan ontology based on the Mercator mapping file (see methods), and subjected to Fisher’s exact test. Bins in red were significantly up-regulated; bins in blue were significantly down-regulated; transcription of bins in white did not change significantly. The results indicate that ontology bins encompassing ET metabolism and signaling are enriched for DE genes in +RB but not in WT at 48 hpi.