Genome-wide gene expression profiles in response to downy mildew in Chinese cabbage (Brassica rapa L. ssp pekinensis)

Downy mildew caused by Hyaloperonospora brassicae is one of the most damaging diseases of Chinese cabbage. In this study, we analyzed genome-wide gene expression profiles of a resistant line 318R and a susceptible line 361S of Chinese cabbage in response to downy mildew infection by high throughput RNA sequencing technology. More transcripts were identified in H. brassicae infected samples in both lines, especially in the susceptible line 361S. A total of 2297 and 3338 differentially expressed genes were identified in 318R and 361S, respectively, which are mainly involved in the plant-pathogen interaction pathway, plant hormone signal transduction pathway, and biosynthesis of secondary metabolites pathway. A total of 1284 genes were found to be differentially expressed in both lines, among which, 68 genes showed higher variation in the resistant line than in the susceptible line. These 68 genes, along with the 1012 genes that were only differentially expressed in the resistant line, were annotated to defense response genes, transcriptional factors, and cell wall related genes, which function in the plant-pathogen interaction pathway, protein processing in endoplasmic reticulum pathway, or metabolism pathways. These genes are important candidates for understanding the molecular mechanisms of host response to downy mildew.