Zhong You 821 Sclerotinia infected vs Mock infected controls in B. napus (Zhong You 821)
Ontology highlight
ABSTRACT:
ORGANISM(S): Brassica napus
PROVIDER: GSE13256 | GEO | 2009/02/01
SECONDARY ACCESSION(S): PRJNA114025
REPOSITORIES: GEO
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Project description:The fungal pathogen Sclerotinia sclerotiorum infects a broad range of dicotyledonous plant species and is the causative agent of stem rot in Brassica napus. To elucidate the mechanisms underlying the defense response, we studied the patterns of gene expression in a partially resistant variety of ZhongYou 821 (ZY821) and a susceptible line from Westar over five time points, 6, 12, 24, 48, and 72 hours post-inoculation (hpi) using a B. napus oligonucleotide microarray. Maximum differential gene expression was observed at 48 hpi in both genotypes with ZY821 responding more quickly than Westar. Specific sets of genes exhibited higher levels of expression at the earlier stages of the infection (6-12 hpi), including genes encoding defense-associated proteins such as chitinases, glucanases, osmotins and lectins and genes encoding transcription factors belonging to the zinc finger, WRKY, AP2, and MYB classes. Genes encoding enzymes involved in JA, ethylene, and auxin synthesis were induced in both genotypes, as were those for gibberellin degradation. Changes in metabolic pathways affecting carbohydrate and energy metabolism appeared to be directed toward shuttling carbon reserves to the TCA cycle. Genes involved in glucosinolate and phenylpropanoid biosynthesis were highly up-regulated suggesting that secondary metabolites are also important components of the response to S. sclerotiorum in B. napus. Keywords: Time course, and infected vs mock infected
2009-02-01 | GSE13254 | GEO
Project description:The fungal pathogen Sclerotinia sclerotiorum infects a broad range of dicotyledonous plant species and is the causative agent of stem rot in Brassica napus. To elucidate the mechanisms underlying the defense response, we studied the patterns of gene expression in a partially resistant variety of ZhongYou 821 (ZY821) and a susceptible line from Westar over five time points, 6, 12, 24, 48, and 72 hours post-inoculation (hpi) using a B. napus oligonucleotide microarray. For each cultivar, a two-dye experiment was run comparing infected to mock-infected stem tissue. For each time point, 6 microarray slides were done (3 biological replicates, with a dye swap for each biological replicate). This SuperSeries is composed of the SubSeries listed below.
2009-02-01 | GSE13262 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE13254: Sclerotinia infected vs Mock infected controls in B. napus (Westar) GSE13256: Zhong You 821 Sclerotinia infected vs Mock infected controls in B. napus (Zhong You 821) The fungal pathogen Sclerotinia sclerotiorum infects a broad range of dicotyledonous plant species and is the causative agent of stem rot in Brassica napus. To elucidate the mechanisms underlying the defense response, we studied the patterns of gene expression in a partially resistant variety of ZhongYou 821 (ZY821) and a susceptible line from Westar over five time points, 6, 12, 24, 48, and 72 hours post-inoculation (hpi) using a B. napus oligonucleotide microarray. For each cultivar, a two-dye experiment was run comparing infected to mock-infected stem tissue. For each time point, 6 microarray slides were done (3 biological replicates, with a dye swap for each biological replicate). Refer to individual Series
2009-01-31 | E-GEOD-13262 | biostudies-arrayexpress
Project description:The fungal pathogen Sclerotinia sclerotiorum infects a broad range of dicotyledonous plant species and is the causative agent of stem rot in Brassica napus. To elucidate the mechanisms underlying the defense response, we studied the patterns of gene expression in a partially resistant variety of ZhongYou 821 (ZY821) and a susceptible line from Westar over five time points, 6, 12, 24, 48, and 72 hours post-inoculation (hpi) using a B. napus oligonucleotide microarray. Maximum differential gene expression was observed at 48 hpi in both genotypes with ZY821 responding more quickly than Westar. Specific sets of genes exhibited higher levels of expression at the earlier stages of the infection (6-12 hpi), including genes encoding defense-associated proteins such as chitinases, glucanases, osmotins and lectins and genes encoding transcription factors belonging to the zinc finger, WRKY, AP2, and MYB classes. Genes encoding enzymes involved in JA, ethylene, and auxin synthesis were induced in both genotypes, as were those for gibberellin degradation. Changes in metabolic pathways affecting carbohydrate and energy metabolism appeared to be directed toward shuttling carbon reserves to the TCA cycle. Genes involved in glucosinolate and phenylpropanoid biosynthesis were highly up-regulated suggesting that secondary metabolites are also important components of the response to S. sclerotiorum in B. napus. Keywords: Time course, and infected vs mock infected Time course experiment (6hr, 12 hr, 24 hr, 48 hr, 72 hrs), sclerotinia infected vs mock-infected. Biological replicates: 3, independently harvested. Technical replicates: 2, dye swapped within each time for each biological replicate (total 6 slides per time point) time after innoculation: 6 hours: westar 6h inf vs control rep1, westar 6h control vs inf rep1, westar 6h inf vs control rep2, westar 6h control vs inf rep2, westar 6h inf vs control rep3, westar 6h control vs inf rep3 time after innoculation: 12 hours: westar 12h inf vs control rep1, westar 12h control vs inf rep1, westar 12h inf vs control rep2, westar 12h control vs inf rep2, westar 12h inf vs control rep3, westar 12h control vs inf rep3 time after innoculation: 24 hours: westar 24h inf vs control rep1, westar 24h control vs inf rep1, westar 24h inf vs control rep2, westar 24h control vs inf rep2, westar 24h inf vs control rep3, westar 24h control vs inf rep3 time after innoculation: 48 hours: westar 48h inf vs control rep1, westar 48h control vs inf rep1, westar 48h inf vs control rep2, westar 48h control vs inf rep2, westar 48h inf vs control rep3, westar 48h control vs inf rep3 time after innoculation: 72 hours: westar 72h inf vs control rep1, westar 72h control vs inf rep1, westar 72h inf vs control rep2, westar 72h control vs inf rep2, westar 72h inf vs control rep3, westar 72h control vs inf rep3 biological replicate: westar 6h inf vs control rep1, westar 6h inf vs control rep2, westar 6h inf vs control rep3 biological replicate: westar 6h control vs inf rep1, westar 6h control vs inf rep2, westar 6h control vs inf rep3 technical replicate - labeled-extract: westar 6h inf vs control rep1, westar 6h control vs inf rep1 technical replicate - labeled-extract: westar 6h inf vs control rep2, westar 6h control vs inf rep2 technical replicate - labeled-extract: westar 6h inf vs control rep3, westar 6h control vs inf rep3 biological replicate: westar 12h inf vs control rep1, westar 12h inf vs control rep2, westar 12h inf vs control rep3 biological replicate: westar 12h control vs inf rep1, westar 12h control vs inf rep2, westar 12h control vs inf rep3 technical replicate - labeled-extract: westar 12h inf vs control rep1, westar 12h control vs inf rep1 technical replicate - labeled-extract: westar 12h inf vs control rep2, westar 12h control vs inf rep2 technical replicate - labeled-extract: westar 12h inf vs control rep3, westar 12h control vs inf rep3 biological replicate: westar 24h inf vs control rep1, westar 24h inf vs control rep2, westar 24h inf vs control rep3 biological replicate: westar 24h control vs inf rep1, westar 24h control vs inf rep2, westar 24h control vs inf rep3 technical replicate - labeled-extract: westar 24h inf vs control rep1, westar 24h control vs inf rep1 technical replicate - labeled-extract: westar 24h inf vs control rep2, westar 24h control vs inf rep2 technical replicate - labeled-extract: westar 24h inf vs control rep3, westar 24h control vs inf rep3 biological replicate: westar 48h inf vs control rep1, westar 48h inf vs control rep2, westar 48h inf vs control rep3 biological replicate: westar 48h control vs inf rep1, westar 48h control vs inf rep2, westar 48h control vs inf rep3 technical replicate - labeled-extract: westar 48h inf vs control rep1, westar 48h control vs inf rep1 technical replicate - labeled-extract: westar 48h inf vs control rep2, westar 48h control vs inf rep2 technical replicate - labeled-extract: westar 48h inf vs control rep3, westar 48h control vs inf rep3 biological replicate: westar 72h inf vs control rep1, westar 72h inf vs control rep2, westar 72h inf vs control rep3 biological replicate: westar 72h control vs inf rep1, westar 72h control vs inf rep2, westar 72h control vs inf rep3 technical replicate - labeled-extract: westar 72h inf vs control rep1, westar 72h control vs inf rep1 technical replicate - labeled-extract: westar 72h inf vs control rep2, westar 72h control vs inf rep2 technical replicate - labeled-extract: westar 72h inf vs control rep3, westar 72h control vs inf rep3
2009-01-31 | E-GEOD-13254 | biostudies-arrayexpress
Project description:The fungal pathogen Sclerotinia sclerotiorum infects a broad range of dicotyledonous plant species and is the causative agent of stem rot in Brassica napus. To elucidate the mechanisms underlying the defense response, we studied the patterns of gene expression in a partially resistant variety of ZhongYou 821 (ZY821) and a susceptible line from Westar over five time points, 6, 12, 24, 48, and 72 hours post-inoculation (hpi) using a B. napus oligonucleotide microarray. Maximum differential gene expression was observed at 48 hpi in both genotypes with ZY821 responding more quickly than Westar. Specific sets of genes exhibited higher levels of expression at the earlier stages of the infection (6-12 hpi), including genes encoding defense-associated proteins such as chitinases, glucanases, osmotins and lectins and genes encoding transcription factors belonging to the zinc finger, WRKY, AP2, and MYB classes. Genes encoding enzymes involved in JA, ethylene, and auxin synthesis were induced in both genotypes, as were those for gibberellin degradation. Changes in metabolic pathways affecting carbohydrate and energy metabolism appeared to be directed toward shuttling carbon reserves to the TCA cycle. Genes involved in glucosinolate and phenylpropanoid biosynthesis were highly up-regulated suggesting that secondary metabolites are also important components of the response to S. sclerotiorum in B. napus. Keywords: Time course, infected vs mock infected Time course experiment (6hr, 12 hr, 24 hr, 48 hr, 72 hrs), sclerotinia infected vs mock-infected. Biological replicates: 3, independently harvested. Technical replicates: 2, dye swapped within each time for each biological replicate (total 6 slides per time point) time after innoculation: 6 hours: zy 6h inf vs control rep1, zy 6h control vs inf rep1, zy 6h inf vs control rep2, zy 6h control vs inf rep2, zy 6h inf vs control rep3, zy 6h control vs inf rep3 time after innoculation: 12 hours: zy 12h inf vs control rep1, zy 12h control vs inf rep1, zy 12h inf vs control rep2, zy 12h control vs inf rep2, zy 12h inf vs control rep3, zy 12h control vs inf rep3 time after innoculation: 24 hours: zy 24h inf vs control rep1, zy 24h control vs inf rep1, zy 24h inf vs control rep2, zy 24h control vs inf rep2, zy 24h inf vs control rep3, zy 24h control vs inf rep3 time after innoculation: 48 hours: zy 48h inf vs control rep1, zy 48h control vs inf rep1, zy 48h inf vs control rep2, zy 48h control vs inf rep2, zy 48h inf vs control rep3, zy 48h control vs inf rep3 time after innoculation: 72 hours: zy 72h inf vs control rep1, zy 72h control vs inf rep1, zy 72h inf vs control rep2, zy 72h control vs inf rep2, zy 72h inf vs control rep3, zy 72h control vs inf rep3 biological replicate: zy 6h inf vs control rep1, zy 6h inf vs control rep2, zy 6h inf vs control rep3 biological replicate: zy 6h control vs inf rep1, zy 6h control vs inf rep2, zy 6h control vs inf rep3 technical replicate - labeled-extract: zy 6h inf vs control rep1, zy 6h control vs inf rep1 technical replicate - labeled-extract: zy 6h inf vs control rep2, zy 6h control vs inf rep2 technical replicate - labeled-extract: zy 6h inf vs control rep3, zy 6h control vs inf rep3 biological replicate: zy 12h inf vs control rep1, zy 12h inf vs control rep2, zy 12h inf vs control rep3 biological replicate: zy 12h control vs inf rep1, zy 12h control vs inf rep2, zy 12h control vs inf rep3 technical replicate - labeled-extract: zy 12h inf vs control rep1, zy 12h control vs inf rep1 technical replicate - labeled-extract: zy 12h inf vs control rep2, zy 12h control vs inf rep2 technical replicate - labeled-extract: zy 12h inf vs control rep3, zy 12h control vs inf rep3 biological replicate: zy 24h inf vs control rep1, zy 24h inf vs control rep2, zy 24h inf vs control rep3 biological replicate: zy 24h control vs inf rep1, zy 24h control vs inf rep2, zy 24h control vs inf rep3 technical replicate - labeled-extract: zy 24h inf vs control rep1, zy 24h control vs inf rep1 technical replicate - labeled-extract: zy 24h inf vs control rep2, zy 24h control vs inf rep2 technical replicate - labeled-extract: zy 24h inf vs control rep3, zy 24h control vs inf rep3 biological replicate: zy 48h inf vs control rep1, zy 48h inf vs control rep2, zy 48h inf vs control rep3 biological replicate: zy 48h control vs inf rep1, zy 48h control vs inf rep2, zy 48h control vs inf rep3 technical replicate - labeled-extract: zy 48h inf vs control rep1, zy 48h control vs inf rep1 technical replicate - labeled-extract: zy 48h inf vs control rep2, zy 48h control vs inf rep2 technical replicate - labeled-extract: zy 48h inf vs control rep3, zy 48h control vs inf rep3 biological replicate: zy 72h inf vs control rep1, zy 72h inf vs control rep2, zy 72h inf vs control rep3 biological replicate: zy 72h control vs inf rep1, zy 72h control vs inf rep2, zy 72h control vs inf rep3 technical replicate - labeled-extract: zy 72h inf vs control rep1, zy 72h control vs inf rep1 technical replicate - labeled-extract: zy 72h inf vs control rep2, zy 72h control vs inf rep2 technical replicate - labeled-extract: zy 72h inf vs control rep3, zy 72h control vs inf rep3
2010-05-06 | E-GEOD-13256 | biostudies-arrayexpress
Project description:Background: Sclerotinia sclerotiorum is one of the most severe fungus diseases in many important crops including sunflower (Helianthus annuus) worldwide. Breeding the resistant varieties are the best strategy to control S. sclerotiorum, however, the molecular regulatory mechanisms of sunflower in response to S. sclerotiorum remain poorly understood. Methods: We performed a leaf transcriptomic analysis to understand the differential defense response to S. sclerotiorum in a disease resistant (DR) genotype and a disease susceptible (DS) genotype of sunflower 24 h post-inoculation. Results: A total of 7439 and 10151 differentially expressed genes (DEGs) were identified in DR and DS genotypes, respectively suggesting that the former is less affected by S. sclerotiorum infection. Pathway analysis revealed that response to S. sclerotiorum was mostly enriched in the DEGs that are involved in the cell wall, redox homeostasis, immune response, protein kinase activity, hormone, transcription factor activities as well as secondary metabolism. The magnitude of expression changes in a set of genes encoding expansins, pectate lyase activities, antioxidant activity and ethylene following S. sclerotiorum infection likely contributed to the different resistance levels of these two genotypes. One gene encoding effector receptor NLR revealing significant opposite expression pattern between DR and DS genotypes along with three hub-genes CDPK9, MAPK5, CML23 by protein-protein interaction (PPI) network analysis were considered as the most possible candidate genes. Conclusion: Our results provide in-depth insights into the molecular mechanisms associated with sunflower defense responses against S. sclerotiorum that will be of great utility in Sclerotinia-resistance breeding.
2022-12-07 | GSE220161 | GEO
Project description:Brassica napus leaves(18 days old) were inoculated by Sclerotinia sclerotiorum with leaves harvested after 12, 24 and 48 h. Arabidopsis thaliana full-genome 70mer microarray representing at least 23,686 genes were used.
2007-10-01 | E-MEXP-1031 | biostudies-arrayexpress
Project description:MicroRNAs are multifunctional non-coding short nucleotide molecules. Nevertheless, the role of miRNAs in the interactions between plants and necrotrophic pathogens is largely unknown. Here, we report the identification of the miRNA repertoire of the economically important oil crop oilseed rape (Brassica napus) and those involved in interacting with its most devastating necrotrophic pathogen Sclerotinia sclerotiorum. We identified 280 B. napus miRNA candidates, including 53 novel candidates and 227 canonical members or variants of known miRNA families, by high-throughput deep sequencing of small RNAs from both normal and S. sclerotiorum-inoculated leaves. Target genes of 15 novel candidates and 222 known miRNAs were further identified by sequencing of degradomes from the two types of samples. MicroRNA microarray analysis revealed that 68 miRNAs were differentially expressed between S. sclerotiorum-inoculated and uninoculated leaves. A set of these miRNAs target genes involved in plant defense to S. sclerotiorum and/or other pathogens such as NBS-LRR R genes and nitric oxygen and reactive oxygen species related genes. Additionally, three miRNAs target AGO1 and AGO2, key components of post-transcriptional gene silencing (PTGS). Expression of several viral PTGS suppressors reduced resistance to S. sclerotiorum. Arabidopsis mutants of AGO1 and AGO2 exhibited reduced resistance while transgenic lines over-expressing AGO1 displayed increased resistance to S. sclerotiorum in an AGO1 expression level-dependent manner. Moreover, transient over-expression of miRNAs targeting AGO1 and AGO2 decreased resistance to S. sclerotiorum in oilseed rape. Our results demonstrate that the interactions between B. napus and S. sclerotiorum are tightly regulated at miRNA level and probably involve PTGS.
2017-05-16 | GSE81560 | GEO
Project description:MicroRNAs are multifunctional non-coding short nucleotide molecules. Nevertheless, the role of miRNAs in the interactions between plants and necrotrophic pathogens is largely unknown. Here, we report the identification of the miRNA repertoire of the economically important oil crop oilseed rape (Brassica napus) and those involved in interacting with its most devastating necrotrophic pathogen Sclerotinia sclerotiorum. We identified 280 B. napus miRNA candidates, including 53 novel candidates and 227 canonical members or variants of known miRNA families, by high-throughput deep sequencing of small RNAs from both normal and S. sclerotiorum-inoculated leaves. Target genes of 15 novel candidates and 222 known miRNAs were further identified by sequencing of degradomes from the two types of samples. MicroRNA microarray analysis revealed that 68 miRNAs were differentially expressed between S. sclerotiorum-inoculated and uninoculated leaves. A set of these miRNAs target genes involved in plant defense to S. sclerotiorum and/or other pathogens such as NBS-LRR R genes and nitric oxygen and reactive oxygen species related genes. Additionally, three miRNAs target AGO1 and AGO2, key components of post-transcriptional gene silencing (PTGS). Expression of several viral PTGS suppressors reduced resistance to S. sclerotiorum. Arabidopsis mutants of AGO1 and AGO2 exhibited reduced resistance while transgenic lines over-expressing AGO1 displayed increased resistance to S. sclerotiorum in an AGO1 expression level-dependent manner. Moreover, transient over-expression of miRNAs targeting AGO1 and AGO2 decreased resistance to S. sclerotiorum in oilseed rape. Our results demonstrate that the interactions between B. napus and S. sclerotiorum are tightly regulated at miRNA level and probably involve PTGS.
2017-05-16 | GSE81561 | GEO
Project description:Global transcriptome profiling of suceptible and tolerant lines of Brassica napus infected with Sclerotinia sclerotiorum using a petal inoculation method that mimics field conditions.
2017-08-01 | GSE81545 | GEO