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Effect of hypoxia on gene expression in Grey poplar

ABSTRACT: The molecular responses of Grey poplar (Populus x canescens) following root hypoxia were studied in roots and leaves using transcript profiling. Grey poplar is a flooding tolerant tree species and analysis of the molecular response to hypoxia may indicate possible adaptation mechanisms to this stress.

ORGANISM(S): Populus sp. Populus tremula x Populus alba

PROVIDER: GSE13109 | GEO | 2009/01/31

SECONDARY ACCESSION(S): PRJNA109943

REPOSITORIES: GEO

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Transcription profiling of grey poplar after hypoxia treatment

Project description:The molecular responses of Grey poplar (Populus x canescens) following root hypoxia were studied in roots and leaves using transcript profiling. Grey poplar is a flooding tolerant tree species and analysis of the molecular response to hypoxia may indicate possible adaptation mechanisms to this stress. Experiment Overall Design: The root system of the poplar trees were flooded for up to 168 h. At three time-points (5 h, 24 h, 168 h) plants were collected and leaf and root tissue analysed separately. At each time-point non-flooded controls were collected and analysed as well.

2009-02-08 | E-GEOD-13109 | biostudies-arrayexpress

Response to drought and salt stress in leaves of poplar (Populus alba × P. glandulosa): Expression profiling by oligonucleotide microarray analysis

Project description:We performed that comprehensive identification of genes responsible for stress tolerance by analyzing the whole-genome expression profiles of poplar (Populus alba × P. glandulosa) leaves exposed to drought and salt stresses. Examination at the molecular level how this tree species responds to drought and salt stresses by regulating the expression of genes involved in signal transduction, transcriptional regulation, and stress responses.

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Poplar tissue types 1

Project description:Global gene expression pattern of different poplar tissue types were determined using a Nimblegen microarray based on JGI v1.1 gene models. All tissue except reproductive tissue were obtained from the same clone used for the poplar genome sequencing project (Populus trichocarpa Nisqually-1). Reproductive tissue were from wild Populus trichocarpa trees.

2010-08-01 | GSE21481 | 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

Expression profiling of in vitro Poplar roots during early interaction with the ectomycorrhizal fungus Laccaria bicolor

Project description:The early phase of the interaction between tree roots and ectomycorrhizal (ECM) fungi, prior to symbiosis establishment, is accompanied by a stimulation of lateral root (LR) development. We set out to identify gene networks that regulate LR development during the early signal exchanges between Populus tremula x Populus alba (hereafter called poplar) and the ECM fungus Laccaria bicolor. A sandwich culture system was developed in order to bring plant and fungus into an indirect contact, which permits signal molecule exchange and LR stimulation (emergence after 4-5 days of contact) but prohibits root colonization. A NimbleGen full genome poplar oligo-array was used to investigate transcript profiles at three days of indirect poplar/L. bicolor contact, referring to the time point of LR initiation in response to the fungus.

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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

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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

Poplar cultivars Soligo and Carpacio

Project description:affy_genomic_poplar - affy_genomic_poplar - The project aims to identify genes of interest for water deficit acclimation in poplar. We look for genes and gene expression networks related to drought stress in two hybrid cultivars, differing in their drought tolerance in field. Affymetrix poplar genome array was designed on several Populus species. In order to deal with comparative approaches, we checked the convenience of the array by hybridizing genomic DNA of the two hybrid cultivars (Populus deltoides × Populus nigra, namely ‘cv Carpaccio’ and ‘cv Soligo’). This point is important as transcript sequence might have diverged in the two genomes (Fossati et al, 2005), which could lead to absence of hybridization without physiological meaning. -Two poplar cultivars, Soligo (S) and Carpacio (C) were grown in controlled conditions. Mature leaves were collected and genomic DNA was extracted from leaves in CTAB buffer. gDNA was fragmented with DNAse1. DNA fragments were labelled with Biotin N6-ddATP and hybridized on Affymetrix poplar genome array. Two technical replicates per genotype were performed. Keywords: genomic comparison,gain of fuction epimutation

2011-04-01 | GSE21334 | GEO

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