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Transcription profiling of poplar WRKY23 reveals a regulatory role in defense: WRKY23-overexpressor

ABSTRACT: To investigate the function of poplar WRKY23, we generated PtWRKY23-overexpressing and -underexpressing (RNAi) plants. Transgenic plants were inoculated with Melampsora rust or mock-inoculated for assessment of rust-resistance and for gene expression profiling using the poplar Affymetrix GeneChipÂ® to study the consequences of PtWRKY23 overexpression and underexpression. Transcriptome analysis of PtWRKY23 overexpressors revealed a significant overlap with the Melampsora-infection response. Transcriptome analysis also indicated that PtWRKY23 affects redox homeostasis and cell wall-related metabolism. Experiment Overall Design: Leaf discs from wildtype, WRKY23-overexpressor and WRKY23-RNAi plants were inoculated with Melampsora medusae f. sp. tremuloidae (Mmt) or were mock-inoculated (control). At five days post-inoculation, tissues were harvested for RNA extraction and hybridization to Affymetrix GeneChipsÂ®. Three biological replications were performed for each line and each inoculation or mock-inoculation. A total of 15 Affymetrix GeneChipsÂ® were used in this study. Data for the WRKY23-overexpressor plants were processed separately from the data for the Mmt-inoculated WRKY23-RNAi plants. The raw data for the Mmt-inoculated wildtype plants were the same in both cases. Experiment Overall Design: This part of the study includes 12 RNA samples consisting of three biological replicates for each of the mock-inoculated or Mmt-inoculated WT and WRKY23-overexpressing plants.

ORGANISM(S): Populus tremula x Populus alba

SUBMITTER: Armand SÃ©guin

PROVIDER: E-GEOD-16417 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription profiling of poplar WRKY23 reveals a regulatory role in defense: WRKY23-RNAi

Project description:To investigate the function of poplar WRKY23, we generated PtWRKY23-overexpressing and -underexpressing (RNAi) plants. Transgenic plants were inoculated with Melampsora rust or mock-inoculated for assessment of rust-resistance and for gene expression profiling using the poplar Affymetrix GeneChipÂ® to study the consequences of PtWRKY23 overexpression and underexpression. Transcriptome analysis of PtWRKY23 overexpressors revealed a significant overlap with the Melampsora-infection response. Transcriptome analysis also indicated that PtWRKY23 affects redox homeostasis and cell wall-related metabolism. Experiment Overall Design: Leaf discs from wildtype, WRKY23-overexpressor and WRKY23-RNAi plants were inoculated with Melampsora medusae f. sp. tremuloidae (Mmt) or were mock-inoculated (control). At five days post-inoculation, tissues were harvested for RNA extraction and hybridization on Affymetrix GeneChipsÂ®. Three biological replications were performed for each line and each inoculation or mock-inoculation. A total of 15 Affymetrix GeneChipsÂ® were used in this study. Data for the Mmt-inoculated WRKY23-RNAi plants were processed separately from the data for the WRKY23-overexpressor plants. The raw data for the Mmt-inoculated wildtype plants were the same in both cases. Normalized data for the Mmt-inoculated wildtype plants that were processed with the Mmt-inoculated WRKY23-RNAi plants are denoted with an "a" suffix. Experiment Overall Design: This part of the study includes 6 RNA samples consisting of three biological replicates for the Mmt-inoculated WT and WRKY23-RNAi (underexpressing) plants.

2009-08-09 | E-GEOD-16419 | biostudies-arrayexpress

Expression profiling and functional analysis of poplar WRKY23 reveals a regulatory role in defense: WRKY23-overexpressor

2009-08-01 | GSE16417 | GEO

Expression profiling and functional analysis of poplar WRKY23 reveals a regulatory role in defense: WRKY23-RNAi

2009-08-01 | GSE16419 | GEO

Identification of rust-induced genes in poplar using Populus 2.0 NimbleGen oligoarray

Project description:Oligoarray expression profiling was carried out in poplar leaves upon infection with rust in order to identify genes expressed during tree defense response. For this purpose, we inoculated detached leaves of the interamerican hybrid poplar Populus trichocarpa x Populus deltoides 'Beaupré' grown in greenhouse either with spores of avirulent strain 93ID6 (incompatible interaction I48) or spores of virulent strain 98AG31 (compatible interaction C48) of the pathogenic rust fungus Melampsora larici-populina. Besides, we mock-inoculated 'Beaupré' leaves with water (control condition, T48). Detached leaves were maintained in vitro in controled conditions to allow fungal infection and colonization of plant tissue. Leaves were sampled 48 hours post-inoculation after that the fungus attempt to penetrate plant cells in mesophyll. Keywords: Plant tissue infection, Plant defense response, Oligonucleotide array

2007-03-15 | GSE7098 | GEO

Identification of rust-induced genes in poplar using Populus PICME 28K cDNA microarrays

Project description:Microarray expression profiling was carried out in poplar leaves upon infection with rust in order to identify genes expressed during tree defense response. For this purpose, we inoculated detached leaves of the interamerican hybrid poplar Populus trichocarpa x Populus deltoides 'Beaupré' grown in greenhouse with spores of avirulent strain 93ID6 of the pathogenic rust fungus Melampsora larici-populina (incompatible interaction, I48). Besides, we mock-inoculated 'Beaupré' leaves with water (control condition, T48). Detached leaves were maintained in vitro in controled conditions to allow fungal infection and colonization of plant tissue. Leaves were sampled 48 hours post-inoculation after that the fungus attempt to penetrate plant cells in mesophyll. Competitive hybridization between transcripts of incompatible interaction (I48) and control condition (T48) was done on Populus PICME 28K cDNA microarray. Keywords: Time-course infection of plant tissue, defense response, cDNA microarray

2007-03-15 | GSE7049 | GEO

Identification of rust-induced genes in poplar using Populus 4.6K cDNA macroarray

Project description:cDNA macroarray expression profiling was carried out in poplar leaves upon infection with rust in order to identify genes expressed during tree defense response. For this purpose, we inoculated detached leaves of the interamerican hybrid poplar Populus trichocarpa x Populus deltoides 'Beaupré' grown in greenhouse either with spores of avirulent strain 93ID6 (incompatible interaction, I) or spores of virulent strain 98AG31 (compatible interaction, C) of the pathogenic rust fungus Melampsora larici-populina. Besides, we mock-inoculated 'Beaupré' leaves with water (control condition, T). Detached leaves were maintained in vitro in controled conditions to allow fungal infection and colonization of plant tissue. Leaves were sampled at 12, 24 and 48 hours post-inoculation (hpi) in a time-course experiment before (12 hpi) and after (24 and 48 hpi) that the fungus attempt to penetrate plant cells in mesophyll. Keywords: Plant tissue infection, Plant defense response, cDNA macroarray

2007-03-15 | GSE7121 | GEO

Transcription analysis by RNAseq of adult wheat after inoculation with Puccinia graminis f. sp. tritici

Project description:The RNA sequencing analysis was undertaken to investigate the transcriptomic changes in adult wheat inoculated with Puccinia graminis f. sp. tritici the causal agent of stem rust disease. The project firstly aims to compare gene expression in one susceptible wheat line with two wheat lines exhibiting adult plant resistance to the stem rust. Secondly, the project aims to examine the temporal changes in gene expression in wheat after inoculation. Wheat plants was grown until maturity under greenhouse conditions. Plants were inoculated with Puccinia graminis f. sp. tritici and the flag leaf sheath sampled for RNA sequencing. The project aims to give essential insight into the adult plant resistance response in wheat to Puccinia graminis f. sp. tritici inoculation.

2022-10-30 | E-MTAB-9681 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Small RNA Mediated Rice Resistance to Xoo

Project description:Purpose: The goal of this study is to identify small non-conding RNAs which are involved in rice resistance to Xoo. Methods: Rice leaves were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). And then, total RNA was extracted to be sequenced using Illumina GAIIx. Results: Using an optimized data analysis workflow to count the expression level of small ncRNA, we found several differentially expressed small ncRNA which may be participated in the interaction between rice and Xoo. Conclusions: Small ncRNA have be found to function in a variety of biological processes. Our study here has showed that several candidate miRNA or siRNA may play a significant role in rice immunity. Plants were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). Samples were collected before inoculation (ck) and at 2, 4, and 24 hours after PXO61 or mock inoculation from Rb49 and MDJ8. Leaf fragments approximately 2 cm in length that were immediately next to the inoculation site were collected.

2016-02-25 | E-GEOD-69242 | biostudies-arrayexpress

Transcription profiling of wheat Lr1- and Lr34-mediated leaf rust resistance in wheat

Project description:The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent of wheat leaf rust. However, the biological basis for the exceptional durability of Lr34 is unclear. The Affymetrix wheat genome array was used to identify wheat genes differentially expressed in a compatible interaction (Tc), an R-gene mediated incompatible interaction (Tc-Lr1), and a race non-specific resistance interaction (Tc-Lr34) in response to infection challenge by P. triticina race 1 at anthesis. Transcriptome interrogation was conducted by comparing mock- and P. triticina-inoculated leaves harvested at 3 and 7 days post inoculation (dpi). SUBMITTER_CITATION: Bolton, M.D., Kolmer, J.A., Xu, W.W., and Garvin, D.F. 2008. Lr34-mediated leaf rust resistance in wheat: transcript profiling reveals a high energetic demand supported by transient recruitment of multiple metabolic pathways. Molecular Plant-Microbe Interactions 21:1515-1527. Experiment Overall Design: The Affymetrix wheat genome array was used to identify wheat genes differentially expressed in a compatible interaction (Tc), an R-gene mediated incompatible interaction (Tc-Lr1), and a race non-specific resistance interaction (Tc-Lr34) in response to infection challenge by P. triticina race 1 at anthesis. Transcriptome interrogation was conducted on leaves harvested at 3 and 7 days post inoculation (dpi). The study utilized a randomized complete block design with three replicates for each genotype, and employed univariate analysis (t-tests) between mock- and P. triticina-inoculated plants within each genotype at each timepoint, for a total of six comparisons across the entire experiment, utilizing a total 36 Affymetrix Wheat Genome Array GeneChips.

2008-11-13 | E-GEOD-9915 | biostudies-arrayexpress

Target genes associated to siRNA mediated repression of Pea3 and Erm transcription factors in mammary cancerous cells

Project description:Pea3 and Erm are transcription factors belonging to the ETS family which are involved in tumorigenesis, particularly mammary oncogenesis. To elucidate the mechanism of Pea3/Erm induced tumorigenesis in mouse mammary cancerous MMT cells (ATCC CCL-51), we have down-regulated Pea3 or Erm expression in this cell line by using small interfering RNA and performed a microarray analysis using Applied Biosystems AB1700 technology to define target associated genes. Keywords: Comparative transcriptome hybridization, small interfering RNA, mouse mammary cancerous cells Mouse mammary cancerous MMT cells (ATCC CCL-51) have been transfected with a siRNA control, an erm-directed siRNA or an pea3-directed siRNA. MMT cells were also used to determine the modifications due to the transfection protocol. These conditions correspond to four sample. Two biological replicate were used for the MMT cells (control sample), three biological replicates were used for the siRNA control (control sample) and erm-directed siRNA (reference sample) MMT cells and four biological replicates were used for the pea3-directed siRNA (reference sample) MMT cells. Transcriptome profiles (28.218 validated mouse genes) were acquired using Applied Biosystems AB1700 technology, which make use of chemiluminescence-based detection chemistry.

2008-08-01 | E-GEOD-6588 | biostudies-arrayexpress

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