A proteome level study in the early stages of clubroot infection in Brassica napus canola.
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ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Brassica Napus (rape)
TISSUE(S): Plant Cell, Root
SUBMITTER: 
Richard Uhrig
LAB HEAD: R. Glen Uhrig
PROVIDER: PXD038670 | Pride | 2024-02-01
REPOSITORIES: Pride
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Project description:Clubroot of Brassicaceae, an economically important soil borne disease, is caused by Plasmodiophora brassicae Woronin, an obligate, biotrophic protist. This disease poses a serious threat to canola and related crops in Canada and around the globe causing significant loss to seed yield. The pathogen is continuously evolving and new pathotypes are emerging, this necessitates the development of novel resistant canola cultivars to manage the disease effectively. Given that proteins play a crucial role in majority of biological processes and molecular functions, the identification of differentially abundant proteins (DAP) using proteomics information is an attractive approach to understand the plant-pathogen interactions as well as in the future development of gene specific markers for developing clubroot resistant (CR) cultivars. In this study, P. brassicae pathotype 3 (P3H) was used to challenge CR and clubroot susceptible (CS) canola lines. Root samples were collected at three distinct stages of pathogenesis, 7-, 14-, and 21-days post inoculation (DPI), protein samples were isolated, digested with trypsin and subjected to LC-MS/MS analysis. A total of 937 proteins demonstrated a significant (q < 0.05) change in abundance in at least in one of the time points when compared between control and inoculated CR-parent, CR-progeny, CS-parent, CS-progeny and 784 proteins were significantly (q < 0.05) changed in abundance in at least in one of the time points when compared between the inoculated- CR and CS root proteomes of parent and progeny across the three time points tested. Functional annotation of the differentially abundant proteins (DAPs) revealed several proteins related to calcium dependent signaling pathways in response to the pathogen. In addition, proteins related to reactive oxygen species (ROS) biochemistry, dehydrins, lignin, thaumatin, and phytohormones were identified. Among the DAPs, 74 putative proteins orthologous to CR proteins and quantitative trait loci (QTL) associated with eight CR loci in four chromosomes including chromosomes A3 and A8 were identified. In conclusion, these results have contributed to an improved understanding of the mechanisms that are involved in mediating response to P. brassicae in canola at the protein level.
2022-03-22 | PXD031070 | Pride
Project description:Clubroot (Plasmodiophora brassicae) is a pathogen of Brassicaceae that causes significant reductions in yield as a consequence of gall formation in the root and hypocotyl of infected plants. The pathogen hijacks host vascular cambium development and cytokinins are implicated in this process. RNASeq was used to investigate changes in cytokinin metabolism during gall formation of clubroot-infected Arabidopsis thaliana. RNASeq analysis of infected tissue showed that host cytokinin metabolism was strongly down-regulated both at the onset (16 DPI) and late (26 DPI) stages of gall formation. Expression of host genes associated with cytokinin biosynthesis, signalling, degradation and conjugation was strongly repressed. Two isopentenyltransferase genes associated with cytokinin biosynthesis are present in the P. brassicae genome and are expressed throughout gall formation.
2016-07-04 | E-MTAB-4176 | biostudies-arrayexpress
Project description:Clubroot (Plasmodiophora brassicae) is a pathogen of Brassicaceae that causes significant reductions in yield as a consequence of gall formation in the root and hypocotyl of infected plants. The pathogen hijacks host vascular cambium development and cytokinins are implicated in this process. Microarray analysis was used to investigate changes in cytokinin metabolism during gall formation of clubroot-infected ipt1;3;5;7 mutants Arabidopsis thaliana. These mutants have severely restricted synthesis of host cytokinins (isopentenyl adenine and trans zeatin) and fail to form a vascular cambium and, as a consequence, do not undergo secondary thickening. Infection of these mutants allows the impact of pathogen-derived cytokinin synthesis to be observed.
2016-01-12 | E-MTAB-4201 | biostudies-arrayexpress
Project description: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, 1,875 and 2,103 genes were found to be up- and down-regulated between CR BJN3-2 and BJN3-2, respectively, at 0, 12, 72, and 96 hours 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.
2016-02-01 | GSE74044 | GEO
Project description:Clubroot (Plasmodiophora brassicae) is a pathogen of Brassicaceae that causes significant reductions in yield as a consequence of gall formation in the root and hypocotyl of infected plants. The pathogen manipulates host cell cycle regulation in order to drive proliferation in early stages of infection and endoreduplication in later stages. Microarrays were used to profile changes in the expression of cell cycle control components at the onset (16 DPI) and late (26 DPI) stages of gall formation.
2023-06-01 | E-MTAB-5599 | biostudies-arrayexpress
Project description:Clubroot disease, caused by Plasmodiophora brassicae, poses a significant global threat to Brassica crop production. Understanding the disease resistance mechanism is vital to assist in the continuous development of clubroot-resistant genetic material. In this study, we used clubroot-resistant (CR) and -susceptible (CS) near-isogenic lines (NILs) of B. napus, carrying resistance of turnip (B. rapa var. rapifera), and conducted transcriptomics and proteomics analysis to characterize the molecular basis of host resistance against clubroot. This study identified genes involved in reactive oxygen species (ROS) scavenging [peroxygenase 3 (BnaA04T0204000WE) and peroxidase 2 (BnaA09T0647200WE)], cell wall modifications [caffeoylshikimate esterase (BnaA04T0244300WE) and shikimate-O-hydroxycinnamoyltransferase (BnaC06T0472200WE)], and glucosinolate biosynthesis [2-oxoglutarate-dependent dioxygenase AOP1 (BnaA01T0266700WE)] that were highly abundant in CR lines. Additionally, disease resistance-related genes, including enhanced disease resistance 2-like (BnaA03T0055600WE) and hairpin-induced family protein YLS9 (BnaA08T0237900WE), were also elevated in the CR lines. In contrast, CS NILs exhibited decreased expression of defense-related genes, increased expression of cell wall-degrading enzymes, and enhanced carbohydrate metabolism, facilitating pathogen proliferation. Integrated analysis of data from the two ‘omics’ approaches showed that the genes related to plant invertase/pectin methylesterase inhibitor (BnaC04T0003100WE), Kelch motif (BnaC02T0374800WE), and laccase (BnaA02T0019200WE) potentially play an important role in host resistance. Antioxidant-related genes such as glucose-6-phosphate dehydrogenase (BnaC09T0029500WE), glutathione S-transferases (BnaA03T0281000WE, BnaA03T0280900WE), catalases (Bnascaffold286T0031400WE), and 4-hydroxyphenylpyruvate dioxygenase (BnaA09T0641500WE) were upregulated in the resistant NILs, potentially protecting cell wall components by ROS scavenging. The identified genes and pathways offer valuable targets for use in breeding aimed at enhancing clubroot resistance.
2025-10-06 | PXD060262 | Pride
Project description:Canola (oilseed rape, Brassica napus L.), is susceptible to infection by the biotrophic protist Plasmodiophora brassicae, the causal agent of clubroot. To understand the roles of microRNAs (miRNAs) during the post-transcriptional regulation of disease initiation and progression, we have characterized the changes in miRNA expression profiles in canola roots during clubroot disease development and have compared these to uninfected roots. Two different stages of clubroot development were targeted in this miRNA profiling study: an early time of 10-dpi for disease initiation and a later 20-dpi, by which time the pathogen had colonized the roots (as evident by visible gall formation and histological observations). P. brassicae responsive miRNAs were identified and validated by qRT-PCR of miRNAs and the subsequent validation of the target mRNAs through starBase degradome analysis, and through 5’ RLM-RACE. This study identifies putative miRNA-regulated genes with roles during clubroot disease initiation and development. Putative target genes identified in this study included: transcription factors (TFs), hormone-related genes, as well as genes associated with plant stress response regulation such as cytokinin, auxin/ethylene response elements. The results of our study may assist in elucidating the role of miRNAs in post-transcriptional regulation of target genes during disease development and may contribute to the development of strategies to engineer durable resistance to this important phytopathogen.
2013-11-28 | GSE51590 | GEO
Project description:Clubroot disease, caused by Plasmodiophora brassicae Woronin, leads to substantial yield losses in Brassica crops worldwide, including Chinese cabbage. Nevertheless, the molecular mechanisms underlying host defense responses remain poorly understood. In this study, we assessed clubroot resistance by comparing the resistant line ‘CR Jingqiu Xinsanhao’ (JQX3) with the susceptible cultivar ‘Zhongbai 76’ (ZB76) through histological analysis of root tissues and monitoring of disease progression in pot trials. Integrated transcriptomic and metabolomic approaches were employed to characterize the defense mechanisms of JQX3 against P. brassicae infection. Marked metabolic reprogramming was detected during both the primary (3 days after inoculation, DAI) and secondary (10 DAI) infection stages. Four pathways—tyrosine metabolism, phenylpropanoid biosynthesis, valine, leucine and isoleucine biosynthesis, and glucosinolate biosynthesis—were significantly enriched at both time points. Notably, differential expression of key enzymatic genes and accumulation of intermediates in the lignin biosynthesis pathway underscored the importance of lignification in the JQX3–P. brassicae interaction. Furthermore, the intermediates p-coumaric acid and coniferaldehyde markedly inhibited P. brassicae spore germination, demonstrating their direct antifungal activity and potential as natural agents for disease control. These findings elucidate key defense-related pathways in Chinese cabbage and offer valuable insights for the development of sustainable clubroot management strategies.
2025-09-14 | GSE307500 | GEO
Project description:The clubroot disease caused by the obligate biotrophic protist Plasmodiophora brassicae on host plants of the Brassicaceae family is characterized by enhanced cell division and cell expansion. Since a typical root section of an infected plant always includes different stages of the pathogen as well as uninfected cells, we were interested to investigate specific developmental stages of the pathogen and their effect on host transcriptional changes. We extended previous microarray studies on whole roots by using Laser Microdissection and Pressure Catapulting (LMPC) to isolate individual cells harboring defined developmental stages of the pathogen. In addition, we compared the central cylinder of infected to contol plants. We were especially interested to elucidate the stage-specific hormonal network. The upregulation of genes involved in auxin and cytokinin metabolism and signaling was confirmed. In addition, we found evidence that brassinosteroid (BR) synthesis and signal perception was in many cases upregulated in enlarged cells and the central cylinder. This was confirmed by qPCR and mutant analysis of the BR receptor mutant bri1-6, which exhibited less severe gall formation than the respective wild type. Our results identify novel hormone pathways involved in clubroot development. Using this method of single cell preparation combined with transcriptome analysis has been very useful to elucidate the regulation of gall growth by this obligate biotropic pathogen in a cell- and stage-specific manner. Transcription profiling was performed in isolated Arabidopsis thaliana root cells harboring different developmental stages of Plasmodiophora brassicae at two time points after inoculation (dai) (14 and 21 dai), as well as in infected central cylinder tissue from roots at 14 dai (days after inoculation). Control samples were taken from uninfected roots. Host cells were dissected from paraffin embedded roots using Laser Microdissection and Pressure Catapulting (LMPC). 8 samples have been analyzed.
2014-02-23 | E-GEOD-44676 | biostudies-arrayexpress
Project description:Canola (oilseed rape, Brassica napus L.), is susceptible to infection by the biotrophic protist Plasmodiophora brassicae, the causal agent of clubroot. To understand the roles of microRNAs (miRNAs) during the post-transcriptional regulation of disease initiation and progression, we have characterized the changes in miRNA expression profiles in canola roots during clubroot disease development and have compared these to uninfected roots. Two different stages of clubroot development were targeted in this miRNA profiling study: an early time of 10-dpi for disease initiation and a later 20-dpi, by which time the pathogen had colonized the roots (as evident by visible gall formation and histological observations). P. brassicae responsive miRNAs were identified and validated by qRT-PCR of miRNAs and the subsequent validation of the target mRNAs through starBase degradome analysis, and through 5M-bM-^@M-^Y RLM-RACE. This study identifies putative miRNA-regulated genes with roles during clubroot disease initiation and development. Putative target genes identified in this study included: transcription factors (TFs), hormone-related genes, as well as genes associated with plant stress response regulation such as cytokinin, auxin/ethylene response elements. The results of our study may assist in elucidating the role of miRNAs in post-transcriptional regulation of target genes during disease development and may contribute to the development of strategies to engineer durable resistance to this important phytopathogen. In this miRNA-microarray experiment a total of 4 samples were analyzed with their 3 biological replicates. In which 2 samples C 10 DAY and C 20 DAY was used as referrence contols.
2013-11-28 | E-GEOD-51590 | biostudies-arrayexpress