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Rewatering-Global gene expression in young differentiating xylem of poplar in response to a drought –rewatering cycle

ABSTRACT: 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

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

PROVIDER: GSE20061 | GEO | 2010/06/03

SECONDARY ACCESSION(S): PRJNA124201

REPOSITORIES: GEO

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rewatering-Global gene expression in young differentiating xylem of poplar in response to a drought ârewatering cycle

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

xyleme-Molecular bases of acclimation and adaptation to water deficit in poplar.

Project description:affy_popsec_orleans_poplar - xyleme - This project aims to identify candidate genes for water deficit acclimation and/or adaptation in a tree species: poplar. Due to compelling evidence that transcriptional regulation plays a major role in regulating many biological processes, we will look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in two poplar genotypes of contrasted tolerance to water deficit, at various stages and intensities of stress and simultaneously in whole xylem and cambial zone from young trees. The co-analysis of two genotypes of contrasted tolerance to water deficit should allow to better discriminating genes presenting a potential adaptative character from genes responding passively to the constraint. The consideration of both whole xylem and cambial zone will enable us to discriminate between regulations events originating from very young xylem cells undergoing their first steps of xylem differentiation (cambial zone) compared to whole xylem sample enriched in more differentiated xylem cells and parenchyma ray cells.-Two poplar clones, named Soligo (S) and Carpaccio (C) were submitted to 4 treatments: non-stressed control, severe-drought stress, mild-drought stress and early-drought stress. Two pools of 2 or 3 trees were considered as biological replicates. Two different samples were collected on each individual tree: whole stem xylem (X) and cambial zone plus very young expanding xylem (Y). Total RNAs were extracted from each tree and assemble in pool of 3 or 2 individuals using equimolar ratio for each X and for Y. One affymetrix slide corresponds to one pooled RNA sample (X or Y). A total number of slides : 4 treatments x 2 clones x 2 tissues x 2 biological replicates (pool) = 32 slides, will be done. Keywords: genotype and ecotype comparison,organ comparison,treated vs untreated comparison

2012-12-15 | GSE17220 | GEO

xyleme-Molecular bases of acclimation and adaptation to water deficit in poplar.

2012-12-15 | E-GEOD-17220 | biostudies-arrayexpress

gravitropic stimulation / isotropic light-Characterization of early molecular events of woody stem gravitropism independently of phototropic responses

Project description:12plex_poplar_2012-01 - gravitropic stimulation / isotropic light - The experiments were designed to identify genes responding to the gravitropic stimulus in the xylem of poplar stem independently of phototropic responses. - young poplar trees were staked one week before use. For the experiment, the plants were placed in an isotropic light environment and were tited at 35° during 30 min. Control plants were kept straight in the isotropic light device. Xylem samples were collected from the upper and lower face of the stems. 4 biological replicates were made (4 controls and 4 tilted plants). RNA was extracted from each xylem sample. cDNA was synthetized. The discovery of genes whose expression is modulated by tilting was performed by a microarray approach.

2016-10-01 | GSE86951 | GEO

circad_pop1-circadian rhythm in the expression of genes involved in the formation of poplar wood

Project description:affy_orleans_circad - circad_pop1 - Global transcriptome analysis of tension wood in poplar over a 24h period. Young differentiating xylem was harvested on the tension wood side of 6 month-old poplar trees grown in greenhouse conditions. The samples were harvested at 6 hour intervals throughout the day. The bioinformatic analysis will permit the identification of genes expressed in tension wood and that cycle with a nycthemeral oscillation pattern. Keywords: time course

2010-06-05 | GSE16459 | GEO

Study of poplar shoot apex transcriptomic response to variations in soil water avaialbility

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

Pilot transcriptomic study- Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

Project description:jc2013_sybiopop_2014-pilot transcriptomic study - Which genes affect biomass yield in poplar? RNA was extracted from young differentiating xylem and cambium collected on 24 4-year-old trees trialed in a common garden experiment at INRA Orléans. The trees corresponded to corresponding to 2 replicates of 12 genotypes from 6 natural populations. After RNA quantification, the RNA from xylem and cambium from the same tree were pooled and subjected to high-throughput sequencing on an Illumina HiSeq 2000 using 100 bp paired-ends reads indexing runs. All the samples were sequenced on one Illumina lane, yielding around 20 million of single-reads per sample.

2018-10-23 | GSE117346 | GEO

circad_pop1-circadian rhythm in the expression of genes involved in the formation of poplar wood

2010-06-16 | E-GEOD-16459 | biostudies-arrayexpress

Transcriptome response to embolism in stems of P. trichocarpa

Project description:Embolism and the refilling of xylem vessels are intrinsic to the ability of plants to handle the transport of water under tension. While the formation of an embolized vessel is an abiotic process, refilling against the pressure gradient requires biological activity to provide both the energy and the water needed to restore xylem transport capacity. We used microarrays to analyze the global transcriptome response of xylem parenchyma cells after embolism formation or infiltration of xylem tissue with sucrose solution.

2011-09-23 | GSE32322 | GEO

Proteomic profile of Pinus pinaster roots under ammonium nutrition

Project description:Ammonium nutrition was studied at short times (24 hours) in roots from one month-old seedlings of maritime pine. Control seedlings were irrigated with 80 mL of water (C) and the experimental seedlings with 80 mL of 3 mM NH4Cl. Root samples were collected at 24 hours post-irrigation and immediately frozen in liquid N. This experiment was carried out three independent times.

2023-03-11 | PXD025331 | Pride

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