Transcriptome Arofile of <i>Brassica rapa</i> L. Reveals the Involvement of Jasmonic Acid, Ethylene, and Brassinosteroid Signaling Pathways in Clubroot Resistance

<i>Plasmodiophora brassicae</i> is a protozoan pathogen that causes clubroot disease in cruciferous plants, particularly Chinese cabbage (<i>Brassica rapa</i>). A previous study identified a clubroot resistance gene (<i>CRd</i>) conferring race-specific resistance to <i>P. brassicae</i>. However, the defense mechanisms of <i>B. rapa</i> against virulent vs. avirulent <i>P. brassicae</i> are poorly understood. In this study, we carried out a global transcriptional analysis in the clubroot-resistant Chinese cabbage inbred line &#8220;85&#8722;74&#8221; carrying the <i>CRd</i> gene and inoculated with avirulent (LAB-4) or virulent (SCCD-52) <i>P. brassicae</i>. RNA sequencing showed that &#8220;85&#8722;74&#8221; responded most rapidly to SCCD-52 infection, and the number of differentially expressed genes was much higher in SCCD-52-treated as compared to LAB-4-treated plants (5552 vs. 304). Transcriptome profiling revealed that plant hormone signal transduction and plant&#8722;pathogen interaction pathways played key roles in the late stages of <i>P. brassicae</i> infection. Genes relating to the salicyclic acid (SA), jasmonic acid (JA)/ethylene (ET), and brassinosteroid (BR) signaling pathways were up-regulated relative to untreated plants in response to LAB-4 infection at 8, 16, and 32 days post-inoculation (dpi) whereas JA, ET, and BR signaling-related genes were not activated in response to SCCD-52, and SA signaling-related genes were up-regulated in both LAB-4 and SCCD-52, suggesting that SA signaling is not the key factor in host resistance to avirulent <i>P. brassicae</i>. In addition, genes associated with phosphorylation and Ca²⁺ signaling pathways were down-regulated to a greater degree following LAB-4 as compared to SCCD-52 infection at 8 dpi. These results indicate that effector-triggered immunity in &#8220;85&#8722;74&#8221; is more potently activated in response to infection with avirulent <i>P. brassicae</i> and that JA, ET, and BR signaling are important for the host response at the late stage of infection. These findings provide insight into <i>P. brassicae</i> pathotype-specific defense mechanisms in cruciferous crops.