Transcriptome analysis of gene expression changes in fer-8 and the parental line

To reveal transcriptional changes in the fer-8 mutant that could explain the increase in Pseudomonas colonization, we performed transcriptional profiling in both shoots and roots from fer-8 and the parental line. We identified 675 up-regulated genes in the shoots of fer-8 relative to wildtype plants. Surprisingly, we found only 82 up-regulated genes in fer-8 roots relative to the parental line, and there were no significantly enriched GO terms. In contrast, we found that the genes upregulated in shoots were enriched in GO terms related to defense, response to fungi, and JA signaling, consistent with previous reports of JA activation in the shoots of another fer mutant fer-4. Overall design: Using RNAseq approach to disect trangscriptome changes in roots and shoots in a novel mutant deficient in feronia receptor like kinase (fer-8).