Brassica napus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA490162 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7814560_1.fastq.gz | Fastqsanger.gz | |||
| SRR7814560_2.fastq.gz | Fastqsanger.gz | |||
| SRR7814570_1.fastq.gz | Fastqsanger.gz | |||
| SRR7814570_2.fastq.gz | Fastqsanger.gz | |||
| SRR7814580_1.fastq.gz | Fastqsanger.gz |
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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: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:Phytohormones control many vital biological processes within plants, including growth and development, senescence, seed setting, fruit ripening and innate immunity. These biological processes are controlled by specific combinations of multiple phytohormones. The three main phytohormones involved in plant innate immunity are salicylic acid (SA), jasmonic acid (JA) and ethylene (ET). SA is produced in response to biotrophic and hemibiotrophic pathogens. Whereas, JA and ET are produced in response to necrotrophic pathogens. Pseudomonas aeruginosa is found ubiquitously within the environment, and has been shown to participate in both beneficial and pathogenic interactions with host plants depending on bacterial strain and environment. In this study, we found that Brassica napus (canola) seedlings infected with P. aeruginosa strain PA14 displayed symptoms of disease and had significant weight loss in both root and shoot. Our transcriptomic data revealed that many molecular processes involved in plant innate immunity were upregulated, whereas photosynthesis was downregulated.
2020-02-14 | E-MTAB-7864 | biostudies-arrayexpress
Project description:477 spring-type Brassica napus (canola) lines from a hybrid breeding programme were genotyped using the Brassica Infinium™ 60k genotyping array.
2023-07-11 | E-MTAB-13142 | 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
Project description:acclimation and deacclimation of two canola varieties
| PRJNA560411 | ENA
Project description:Transcriptome analysis of canola for clubroot resistance
| PRJNA1062990 | ENA
Project description:GBS sequencing of canola from Northern European populations
| PRJNA835738 | ENA
Project description:Drought stress response in canola
| PRJNA743730 | ENA
Project description:62 individual Brassica napus plants of the same accession grown in the same field were expression-profiled in autumn 2016 and phenotyped extensively until harvest in spring 2017. Machine learning models were used to link gene expression to the phenotypes of individual plants, with the purpose of assessing how much phenotype information in encoded in ‘noisy’ gene expression variation among individual plants of the same background grown under the same uncontrolled field conditions. Rosette leaf 8 blades of 62 individual Brassica napus plants of the same winter-type accession (BnASSYST-120, Darmor) grown in the same field (50°58'24.9\\"N 3°46'49.1\\"E, Merelbeke, Belgium) were RNA-seq profiled. No treatments or stresses were applied, all plants were profiled individually under uncontrolled field conditions. Sown at 2016-09-08, rosette leaf 8 sampled for RNA-seq at 2016-11-28, plants harvested at 2017-06-13.
2022-10-10 | E-MTAB-11904 | biostudies-arrayexpress