Study of poplar shoot apex methylome response to variations in soil water avaialbility
Ontology highlight
ABSTRACT:
ORGANISM(S): Populus x canadensis Populus trichocarpa
PROVIDER: GSE46624 | GEO | 2014/01/01
SECONDARY ACCESSION(S): PRJNA201338
REPOSITORIES: GEO
Similar Datasets
Project description:In a context of climate changes, water availability is expected to become a limiting factor for plant growth and to have an impact on forest health. In order to identify genes involved in shoot phenotypic plasticity in response to variations in water availability in trees, gene expression patterns were investigated in the shoot apical meristem (SAM) of Populus deltoides M-CM-^W P. nigra hybrid cuttings submitted to a moderate water deficit followed by a rewatering step. Methylome response was also studied and is another GEO submission. Several gene clusters with expression patterns specific to SAM drought response as well as specific to the rewatering condition could be identified. Among them, genes involved in phytohormone pathways like brassinosteroids were found. Populus deltoides M-CM-^W P. nigra 'Carpaccio' hybrid cuttings were submitted to 3 water conditions: non-limiting, water deficit and water deficit/rewatering cycle (14 days treatment). At the end of the experiment, buds were collected and SAM maually isolated for 6 individuals per condition. Total RNA were independently extracted from 3 individuals per condition and used for microarray analyses.
2014-01-01 | E-GEOD-46605 | biostudies-arrayexpress
Project description:In a context of climate changes, water availability is expected to become a limiting factor for plant growth and to have an impact on forest health. In order to identify genes involved in shoot phenotypic plasticity in response to variations in water availability in trees, DNA methylation patterns were investigated in the shoot apical meristem (SAM) of Populus deltoides M-CM-^W P. nigra hybrid cuttings submitted to a moderate water deficit followed by a rewatering step. Transcriptomic response was also studied and is another GEO submission. Populus deltoides M-CM-^W P. nigra 'Carpaccio' hybrid cuttings were submitted to 3 water conditions: non-limiting, water deficit and water deficit/rewatering cycle (14 days treatment). At the end of the experiment, buds were collected and SAM maually isolated for 6 individuals per condition. DNA was extracted from 3 individuals per condition and pooled. For each condition, methylated DNA was isolated using a MethylDNA Immunoprecipitation (MeDIP) and both total DNA and MeDIP fraction were hybridised to microarrays.
2014-01-01 | E-GEOD-46624 | biostudies-arrayexpress
Project description:In a context of climate changes, water availability is expected to become a limiting factor for plant growth and to have an impact on forest health. In order to identify genes involved in shoot phenotypic plasticity in response to variations in water availability in trees, gene expression patterns were investigated in the shoot apical meristem (SAM) of Populus deltoides × P. nigra hybrid cuttings submitted to a moderate water deficit followed by a rewatering step. Methylome response was also studied and is another GEO submission. Several gene clusters with expression patterns specific to SAM drought response as well as specific to the rewatering condition could be identified. Among them, genes involved in phytohormone pathways like brassinosteroids were found.
2014-01-01 | GSE46605 | GEO
Project description:Transcriptome profiling in response to water stress and rewatering of Moricandia species with C3 and C3-C4 intermediate photosynthesis.
2023-02-13 | GSE210653 | GEO
Project description:affy_rewatering_poplar - rewatering - Biological question (15 lines max): Xylogenesis is a complex process and is highly influenced by environmental factors. Numerous studies have shown xylem structural acclimation to moderate and long-lasting water deficits. A decrease in cell lumen size and an increase in vessel density are generally observed. Other preliminary experiments in our laboratory focusing on a short and progressive drought-rewatering cycle in poplar show a gradual decrease in fibre size with decreasing water availability and an important rise in vessel number with irrigation recovery. This suggests a reorientation during the early stages of cambial derivatives differentiation towards vessel formation. The aim of this study is to characterize global gene expression in young differentiating xylem of poplar in response to a drought-rewatering cycle. Results should provide a comprehensive genomic basis for the xylem structural modifications observed.-The experimental design consisted in a differential water supply. Experiments were done on tilted trees to induce tension wood formation. Trees were regularly irrigated at full capacitance until July 18, 2007, the beginning of the experiment. Two sets of plants were designed. For each set, irrigation was withheld until July 25, 2007. At this time, one of the two sets (treated-sample) was re-irrigated at full capacitance during 14hrs (WDR) while the other one was maintained under water deficit (WD). Samples were collected after the 14hrs for all trees. Keywords: treated vs untreated comparison
2010-06-03 | GSE20061 | GEO
Project description:affy_rewatering_poplar - rewatering - Biological question (15 lines max): Xylogenesis is a complex process and is highly influenced by environmental factors. Numerous studies have shown xylem structural acclimation to moderate and long-lasting water deficits. A decrease in cell lumen size and an increase in vessel density are generally observed. Other preliminary experiments in our laboratory focusing on a short and progressive drought-rewatering cycle in poplar show a gradual decrease in fibre size with decreasing water availability and an important rise in vessel number with irrigation recovery. This suggests a reorientation during the early stages of cambial derivatives differentiation towards vessel formation. The aim of this study is to characterize global gene expression in young differentiating xylem of poplar in response to a drought-rewatering cycle. Results should provide a comprehensive genomic basis for the xylem structural modifications observed.-The experimental design consisted in a differential water supply. Experiments were done on tilted trees to induce tension wood formation. Trees were regularly irrigated at full capacitance until July 18, 2007, the beginning of the experiment. Two sets of plants were designed. For each set, irrigation was withheld until July 25, 2007. At this time, one of the two sets (treated-sample) was re-irrigated at full capacitance during 14hrs (WDR) while the other one was maintained under water deficit (WD). Samples were collected after the 14hrs for all trees. Keywords: treated vs untreated comparison 6 arrays - poplar
2010-06-16 | E-GEOD-20061 | biostudies-arrayexpress
Project description:affy_popsec_nancy_pophydro_roots_poplar - This project aims to identify genes of interest for control of root growth in response to water deficit in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in root apices of cuttings grown in hydroponics and osmotically stressed with PEG. Root apex is the location of root elongation and these analyses intend to identify genes involved in the control of cell expansion and thus of root elongation. Indeed, root growth maintenance in response to water shortage contributes to plant tolerance to water deficit.-Poplar cuttings (cv Soligo) were grown in hydroponics. A moderate water deficit was applied by adding PEG to the nutrient solution (200g/l). After 3 days, the apex (1 cm-long) of the roots of each cutting were collected. For control and stressed treatments, RNAs were extracted from two pools of 5 to 9 roots (issued from 2 to 5 cuttings). A pool is considered as one biological replicate and corresponds to one Affymetrix slide. Keywords: treated vs untreated comparison
2011-01-15 | GSE17225 | GEO
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
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 4 arrays - poplar
2011-04-01 | E-GEOD-21334 | biostudies-arrayexpress
Project description:affy_popsec_nancy_pophydro_roots_poplar - This project aims to identify genes of interest for control of root growth in response to water deficit in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in root apices of cuttings grown in hydroponics and osmotically stressed with PEG. Root apex is the location of root elongation and these analyses intend to identify genes involved in the control of cell expansion and thus of root elongation. Indeed, root growth maintenance in response to water shortage contributes to plant tolerance to water deficit.-Poplar cuttings (cv Soligo) were grown in hydroponics. A moderate water deficit was applied by adding PEG to the nutrient solution (200g/l). After 3 days, the apex (1 cm-long) of the roots of each cutting were collected. For control and stressed treatments, RNAs were extracted from two pools of 5 to 9 roots (issued from 2 to 5 cuttings). A pool is considered as one biological replicate and corresponds to one Affymetrix slide. Keywords: treated vs untreated comparison 4 arrays - poplar
2011-01-15 | E-GEOD-17225 | biostudies-arrayexpress