Root RNA-seq analysis reveals a distinct transcriptome landscape between clubroot-susceptible and clubroot-resistant Chinese cabbage lines after Plasmodiophora brassicae infection

Abstract

Clubroot, caused by the soil-borne protist Plasmodiophora brassicae, is considered as one of the most economically important diseases of Brassica crops worldwide. The Chinese cabbage (Brassica rapa ssp. pekinesis) doubled haploid (DH) line R635–10 was previously identified resistant to the pathogen P. brassicae, but contrastly the line S177–47 was obviously sensitive to this pathogenic infection. The goal of this study was to reveal the molecular mechanisms related to distinct responses by resistant line R635–10 and susceptible line S177–47 to the pathogen treatment. In the present work the differentially expression genes (DEGs) were firstly revealed by RNA-seq analysis between B. rapa resistant line R635–10 and susceptible line S177–47 before and after P. brassicae infection, and functional analysis of these identified DEGs was performed with the Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis etc. We identified 2089 DEGs in the resistant line R635–10 after P. brassicae infection, and among the identified DEGs enriched in metabolic process, biological regulation, response to stimulus, plant-pathogen interaction, plant hormone signal transduction, the genes related to disease-resistance, calcium ion influx, glucosinolate biosynthesis, cell wall thickening, salicylic acid (SA) homeostasis, chitin metabolism, pathogenesis-related (PR) pathway, etc. were largely up-regulated in the resistant line R635–10, which coincided with the recent results released elsewhere. However, in contrast, a vast number of 10,038 DEGs were obtained in the susceptible line S177–47 after infection, among which the up-regulated genes were annotated with DNA replication, citrate cycle (TCA cycle), oxidative phosphorylation, cell wall expansion and nodulin-relatedness, which were mostly concerned with cell cycle control and cell division, and energy production and conversion. In addition, the Indole acetic acid (IAA) and cytokinin-related genes were also obviously upregulated in the susceptible line S177–47, which probably affected the uncontrolled cell division and root swelling in the clubroot development. Our results provide comprehensive insights into the transcriptomic landscape to reveal molecular mechanisms concerned with pathogen resistance and / or susceptibility after P. brassicae infection in two different Chinese cabbage lines.