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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome Analysis of Populus x canadensis in Response to Drought Stress

ABSTRACT: To investigate the response of poplar hybrids to drought, leaves were collected from plants to which water was suspended for 8 and 13 days. After measuring the respective relative water content, RNAs were isolated from leaves of moderately and severely droughted plants and from control plants, and Illumina RNA sequencing was performed to analyze RNA synthesis in these tissues. Transcriptional profiling of leaves of poplar plants subjected to 8 or 13 days of water deprivation. Sequence data were generated by deep sequencing, on four replicates (2 per 2 hybrids), using Illumina HiSeq2000.

ORGANISM(S): Populus x canadensis

SUBMITTER: Elena Barghini

PROVIDER: E-GEOD-64044 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome Analysis of Populus x canadensis in Response to Drought Stress

Project description:To investigate the response of poplar hybrids to drought, leaves were collected from plants to which water was suspended for 8 and 13 days. After measuring the respective relative water content, RNAs were isolated from leaves of moderately and severely droughted plants and from control plants, and Illumina RNA sequencing was performed to analyze RNA synthesis in these tissues.

2015-01-21 | GSE64044 | GEO

Expression data from one-year-old leaves of Populus simonii treated with short-term water deficit

Project description:We take one-year-old plants for short-term water deficit treatments and controls. We use the Affymetrix Poplar GeneChip to decrypt the gene functions and mechanisms in Populus simonii leaves and detail the global program of gene expression during water deficit treatments. Populus simonii leaves were taken from short-term water-deficit-treated plants and control plants for RNA extraction and hybridization on Affymetrix microarrays. D1 and D2 are from water-deficit-treated plants, CK1 and CK2 are controls.

2012-04-26 | E-GEOD-37608 | biostudies-arrayexpress

Response to drought and salt stress in leaves of poplar (Populus alba M-CM-^W 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 M-CM-^W 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. Genome-wide analysis was conducted in poplar leaves exposed to drought and salt stresses.The plants were acclimated in soil and grown for 6 weeks in controlled conditions in a growth room (16 h light; light intensity, 150 M-NM-<mol m-2sec-1; 24M-BM-0C). Plants with a height of about 15 cm were separately exposed to either drought or salt stress. Up- and down-regulated genes were identified, and their putative functions are discussed.

2014-08-12 | E-GEOD-60311 | biostudies-arrayexpress

Expression data from one-year-old leaves of Populus simonii treated with short-term water deficit

2012-04-27 | GSE37608 | GEO

Expression profiling of soybean genes in response to drought (reproductive stage)

Project description:Drought-responsive genes in soybean leaves were successfully identified using Affymetrix Soybean Gene 1.0 ST arrays on leaves samples of reproductive-stage soybean plants. R1 soybean plants planted in pots were imposed drought by withholding water for 5 days until the soil moisture content dropped to 5%, and 3rd trifoliates (now at the R2 stage) were collected for expression profiling. Soybean plants were grown in pots. When the plants reached the R1 stage (started flowering), drought treatment was imposed by withholding water. The soil moisture content was monitored during the process until the 5th day of water withholding, when soil moisture content reached 5%. The 3rd trifoliate (counting from shoots), now at the R2 stage, was collected for total RNA extraction, while other 3rd trifoliates of similar chlorophyl index were collected for leaves water content determination to identify the severity of the stress. Total RNA from 3rd trifoliates were used for expression profiling using Affymetrix Soybean Gene 1.0 ST arrays. Four biological repeats per treatment were performed, three biological repeats were chosen for expression profiling.

2012-11-10 | E-GEOD-40604 | biostudies-arrayexpress

RNAi-mediated downregulation of poplar plasma membrane intrinsic proteins (PIPs) changes plasma membrane proteome composition and affects leaf physiology

Project description:Plasma membrane intrinsic proteins (PIPs) are one subfamily of aquaporins that mediate the transmembrane transport of water. To reveal their function in poplar, we generated transgenic poplar plants in which the translation of PIP genes was downregulated by RNA interference investigated these plants with a comprehensive leaf plasma membrane proteome and physiome analysis. First, inhibition of PIP synthesis strongly altered the leaf plasma membrane protein composition. Strikingly, several signaling components and transporters involved in the regulation of stomatal movement were differentially regulated in transgenic poplars. Furthermore, hormonal crosstalk related to abscisic acid, auxin and brassinosteroids was altered, in addition to cell wall biosynthesis/cutinization, the organization of cellular structures and membrane trafficking. A physiological analysis confirmed the proteomic results. The leaves had wider opened stomata and higher net CO2 assimilation and transpiration rates as well as greater mesophyll conductance for CO2 (gm) and leaf hydraulic conductance (Kleaf). Based on these results, we conclude that PIP proteins not only play essential roles in whole leaf water and CO2 flux but have important roles in the regulation of stomatal movement.

2015-08-10 | PXD002544 | Pride

Expression profiling of soybean genes in response to drought

Project description:Drought-responsive genes in soybean leaves were successfully obtained using soybean gene 1.0 ST array. Leaf samples from the vegetative stage of soybean plants were used. V6 soybean plants planted in the pots were imposed drought by withholding water for 6 days until the soil moisture content drop to 5% and trifolium 4th were collected for expression profiling

2012-04-02 | E-GEOD-29663 | biostudies-arrayexpress

affy_popsec_nancy_leaves2007_poplar -Molecular bases of acclimatation and adaptation to water deficit in poplar

Project description:affy_popsec_nancy_leaves_poplar - affy_popsec_nancy_leaves2007_poplar - This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in mature leaves, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. During water deficit, leaves underwent many processes aiming to maintain cells integrity such as water status adjustment through osmoregulation or cell detoxication. These analyses intend to identify genes of interest involved in homeostasis maintenance. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to discriminate genes presenting a potential adaptative character from genes responding passively to the constraint-In a first experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 4 treatments: control, mild water deficit, moderate water deficit (12-day long for both) and early-drought stress (about 36-h long). Growth and physiology was characterised on a batch of plants and samples collected on another batch of plants. In a second experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 2 treatments: control and moderate water deficit. Mature leaves were collected and total RNAs were extracted from each tree individually. Two pools of 3 (or 2) individuals were made using equimolar ratio. A pool is considered as one biological replicate and corresponds to one Affimetrix slide. Keywords: treated vs untreated comparison

2011-01-15 | GSE17230 | GEO

affy_popsec_nancy_leaves2008_poplar -Molecular bases of acclimatation and adaptation to water deficit in poplar

Project description:affy_popsec_nancy_leaves_poplar - affy_popsec_nancy_leaves2008_poplar - This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in mature leaves, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. During water deficit, leaves underwent many processes aiming to maintain cells integrity such as water status adjustment through osmoregulation or cell detoxication. These analyses intend to identify genes of interest involved in homeostasis maintenance. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to discriminate genes presenting a potential adaptative character from genes responding passively to the constraint-In a first experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 4 treatments: control, mild water deficit, moderate water deficit (12-day long for both) and early-drought stress (about 36-h long). Growth and physiology was characterised on a batch of plants and samples collected on another batch of plants. In a second experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 2 treatments: control and moderate water deficit. Mature leaves were collected and total RNAs were extracted from each tree individually. Two pools of 3 (or 2) individuals were made using equimolar ratio. A pool is considered as one biological replicate and corresponds to one Affymetrix slide. Keywords: treated vs untreated comparison

2011-01-15 | GSE17226 | GEO

Expression data from leaves of GA-deficient and GA-insensitive transgenic poplar

Project description:We used whole-genome microarrays to identify differentially expressed genes in leaves of GA-deficient (35S::PcGA2ox) and/or GA-insensitive (35S::rgl1) transgenics as compared to WT poplar (717-1B4 genotype). Our work suggests that the molecular machinery that reduces gibberellins (GAs) concentration and signaling is a major route for restraining growth under both immediate and imminent adverse conditions. We show that inhibition of growth as a result of water deprivation and short days (SDs) coincides with up-regulation of several DELLA and GA2ox encoding genes in poplar. Likewise, GA-deficient and GA-insensitive transgenics, with up-regulated GA2ox and DELLA domain proteins, elicited a hypersensitive growth inhibition in response to both drought and SDs. Because the GA-modified transgenic showed accelerated response to drought and SD, we hypothesized that the mechanisms associated with these responses are constitutively elevated even under control conditions (well-watered, long day photoperiod). Therefore, we used whole-genome poplar microarray to study transcriptome level changes in the leaves of transgenic compared to WT plants grown under control environment. Genetic background for all plants was INRA 717-1B clone (Populus tremula x Populus alba). Expression analysis was preformed on three individual genotypes; wild-type (WT, untransformed control), 35S::PcGA2ox and 35S::rgl1. Leaves from two independent biological replicates per genotype were used, each pooled from 20 clonally propagated plants.

2014-01-01 | E-GEOD-38390 | biostudies-arrayexpress

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