Transcriptome Analysis of Brassica rapa Near-Isogenic Lines Carrying Clubroot-Resistant and –Susceptible Alleles in Response to Plasmodiophora brassicae during Early Infection

Abstract

Although Plasmodiophora brassicae is one of the most common pathogens worldwide, the causal agent of clubroot disease in Brassica crops, resistance mechanisms to it are still only poorly understood. To study the early defense response induced by P. brassicae infection, a global transcriptome profiling of the roots of two near-isogenic lines (NILs) of clubroot-resistant (CR BJN3-2) and clubroot-susceptible (BJN3-2) Chinese cabbage (Brassica rapa) was performed by RNA-seq. Among the 42,730 unique genes mapped to the reference genome of B. rapa, 1875, and 2103 genes were found to be up- and down-regulated between CR BJN3-2 and BJN3-2, respectively, at 0, 12, 72, and 96 h after inoculation (hai). Functional annotation showed that most of the differently expressed genes are involved in metabolism, transport, signal transduction, and defense. Of the genes assigned to plant-pathogen interactions, 151 showed different expression patterns between two NILs, including genes associated with pathogen-associated molecular patterns (PAMPs) and effectors recognition, calcium ion influx, hormone signaling, pathogenesis-related (PR) genes, transcription factors, and cell wall modification. In particular, the expression level of effector receptors (resistance proteins), PR genes involved in salicylic acid (SA) signaling pathway, were higher in clubroot-resistant NIL, while half of the PAMP receptors were suppressed in CR BJN3-2. This suggests that there was a more robust effector-triggered immunity (ETI) response in CR BJN3-2 and that SA signaling was important to clubroot resistance. The dataset generated by our transcriptome profiling may prove invaluable for further exploration of the different responses to P. brassicae between clubroot-resistant and clubroot-susceptible genotypes, and it will strongly contribute to a better understanding of the molecular mechanisms of resistance genes of B. rapa against P. brassicae infection.

Comparative Transcriptome Analysis between Broccoli (Brassica oleracea var. italica) and Wild Cabbage (Brassica macrocarpa Guss.) in Response to Plasmodiophora brassicae during Different Infection Stages

“…Microscopic observations revealed that root–hair infection (7 DAI) and cortical infection (14 DAI) were both present in B2013 and 90196 ( Figure 1 ). This finding was not in agreement with previous studies (Feng et al, 2013; Chen et al, 2016), in which secondary infection did not occur in resistant lines, possibly due to qualitative resistance under single-gene control.…”

“…The results showed that the JA pathway was weakly activated in the resistant genotype but strongly induced in the susceptible genotype, in agreement with results reported for Arabidopsis by Lemarié et al (2015). Chen et al (2016) also demonstrated that the SA signaling pathway, but not the JA/ET signaling pathway, played a critical role in B. rapa resistance to P. brassicae infection. Jubault et al (2013) also found that both the SA and ET pathways were induced during the partial resistance response, whereas the JA pathway was repressed.…”

“…To date, studies of the molecular basis of clubroot resistance from Brassica crops mainly focused on qualitative resistance, especially in Chinese cabbage (Chen et al, 2016) and canola (Chu et al, 2014). However, illuminating molecular mechanism of quantitative resistance could lead to insight into the relationship between qualitative and quantitative resistance, thus to guild utilization of the two types to produce durably resistant cultivar (Jubault et al, 2013).…”

“…In the plant–pathogen interaction pathway, five of the six transcripts homologous to Pseudomonas syringae -resistant Arabidopsis genes were up-regulated in B2013 (one RPS2 , two RPS4 , twp RPS5 , and one RPS6 ), whereas RPS2 was not. It has been reported that RPS4 , RPS5 , and RPS6 could be involved in resistance to P. syringae in A. thaliana (Ade et al, 2007; Kim et al, 2009), while RPS4 and RPS5 may be involved in the resistance interaction between P. brassicae and B. rapa (Chen et al, 2016). One gene encoding a TMV resistance protein was also up-regulated in B2013.…”

“…Chu et al (2014) identified differentially expressed genes (DEGs) involved in the signaling metabolism of jasmonate and ethylene, defensive deposition of callose and the biosynthesis of indole-containing compounds, which were all significantly up-regulated in clubroot-resistant plants compared with susceptible cultivars. More recently, Chen et al (2016) confirmed that genes associated with PAMPs, calcium ion influx, hormone signaling, PR, transcription factors, and cell-wall modification played important roles in host– P. brassicae interactions during the early stages of infection by P. brassicae , based on transcriptome analysis of B. rapa . Xu et al (2016) provided evidence of the involvement of IAA pathway-related genes during the root–hair infection stage in the roots and leaves of B. napus soon after P. brassicae inoculation based on qRT-PCR analysis.…”