A Combined mRNA and microRNA Transcriptome Analysis of B. oleracea Response to Plasmodiophora brassicae Infection

Abstract

Clubroot disease, caused by the pathogen Plasmodiophora brassicae, is a serious disease that poses a critical threat to cabbage production. However, the molecular mechanism of the microRNAs (miRNAs) involved in the cabbage’s response to P. brassicae infection remains to be elucidated. Here, the mRNA and miRNA expression profiles of cabbage in response to a P. brassicae infection were analyzed. In the transcriptome analysis, 2217 and 5552 differentially expressed genes (DEGs) were identified at 7d and 21d after inoculation, which were enriched in MAPK signaling, plant–pathogen interaction, plant hormone signal transduction, and phenylpropanoid biosynthesis pathways. BolC02g057640.2J, BolC09g006890.2J, BolC02g013230.2J, BolC06g006490.2J, BolC03g052660.2J, BolC07g052580.2J, and BolC04g044910.2J were predicted to be significantly involved in the defense response or plant–pathogen interaction through co-expression network analysis. Small RNA data analysis identified 164 miRNAs belonging to 51 families. miR1515, miR166, miR159, and miR9563 had the greatest number of members among the miRNA families. Integrated analysis revealed 23 miRNA–mRNA interactions related to a P. brassicae infection. The target genes of differentially expressed miRNAs (DEMs) revealed the NAC, ARF, TCP, and SPL transcription factor members that probably participate in the defense response. This study provided new insights into the miRNA-involved regulatory system during the process of disease infection with P. brassicae in cabbage.