Gene expression changes in response to drought stress in Arabidopsis reveal early responses leading to acclimation in plant growth
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE24177 | GEO | 2010/10/01
SECONDARY ACCESSION(S): PRJNA130099
REPOSITORIES: GEO
Similar Datasets
Project description:Plant drought stress response and resistance are complex biological processes that merit systems-level analyses to dissect drought stress encountered by crops in the field. We have used gene expression profiling of Arabidopsis plants subjected to a controlled, sublethal, moderate drought (mDr) treatment to characterize early and late response to drought. We have also compared these profiles to those from plants treated with soil water deficit (progressive) drought (pDr) to reveal acclimation responses in plants. Controlled moderate drought (mDr) was maintained by giving Arabidopsis (Columbia) plants water to keep the soil moisture level at 30% of field capacity, which is 200% or 2 g H2O g-1 dry soil. Water was withheld at 30 days after sowing (DAS). For progressive drought (pDr) treatment, plants were grown in a growth room as described above, water was withheld at 35 DAS, and were allowed to dry until the required pDr level was reached. For RNA isolation, two biological replicate samples of 5 pooled plants were collected at early (day1) and late stage (day10) for mDr, and first day of wilting for pDr, along with controls for mDr and pDr. Samples were hybridized to the Affymetrix (ATH1 25K) GeneChip.
2010-10-01 | E-GEOD-24177 | biostudies-arrayexpress
Project description:Drought is one of the most important environmental fluctuations affecting tree growth and survival. Therefore, understanding of physiological and transcriptomic responses of trees to this stress factor will make important contributions to forest health and productivity. Here, we report comparative physiological and microarray based transcriptome analysis between drought resistant (N.62.191) and drought-sensitive (N.03.368.A) black poplar genotypes under well-watered (WWP), moderate drought (MD), severe drought (SD) and post drought re-watering (PDR) conditions. In the study, sensitive genotype exhibited a drought escape strategy with lower leaf water potential, higher reactive oxygen production, complete leaf abscission and subsequent terminal shoot necrosis under drought stress. On the other hand, resistant genotype had a dehydration tolerance indicating highly delayed leaf abscission under drought and fast growing capacity during re-watering conditions. Gene ontology enrichment analysis attributed drought susceptibility of black poplar to significant up-regulation of genes functional in transcription regulation (AP2/ERF, NAC and WRKY), cell wall modification (Expansins), fatty acid metabolism (enoyl-ACP reductase, lipid transport protein particle), protein degradation (endopeptidases), ethylene synthesis (1-aminocyclopropane-1-carboxylate) and riboflavin synthesis (GTP cyclohydrolase II) under drought stress. Transcriptomic comparison indicated significant down-regulation of photosynthesis, electron transport and carbohydrate metabolism related genes under drought stress in sensitive genotype. Although, similar reduction in carbohydrate metabolism was also recorded for resistant genotype, genes related with photosynthesis and electron transport systems were not down regulated even under SD for this genotype. Resistant genotype specific up-regulation of small heat shock proteins (sHSP) and bark storage proteins revealed importance of protein protection and nitrogen remobilization under drought stress, respectively. This is the first study associating BSP production to delayed leaf abscission and drought tolerance in trees. For Microarray experiment total RNA was isolated from the leaves randomly selected from two balck poplar seedlings (two biological replicates) for resistant and sensitive genotypes at well watered period (WWP), moderate drought (MD), severe drought (SD) and post drought rewatering (PDR) periods. For each water availability regime total isolated RNA was loaded onto two Affymetrix poplar Gene Chips for each genotype. Totally 16 Affymetrix poplar GeneChips (2 genotypes × 4 water availability regimes × 2 biological replicates) were used for transcriptional analysis.
2015-06-15 | E-GEOD-69875 | biostudies-arrayexpress
Project description:With frequent fluctuations in global climate, plants often experience co-occurring dry-wet cycles and pathogen infection and this combination adversely affects plant survival. In the past, some studies indicated that morpho-physiological responses of plants to the combined stress are different from the individual stressed plants. However, interaction of drought stressed or drought recovered plants with pathogen has not been widely studied at molecular level. Such studies are important to understand the defense pathways that operate as part of combined stress tolerance mechanism. In this study, Arabidopsis plants were exposed to individual drought stress (soil drying at 40% FC, D), Pseudomonas syringae pv tomato DC3000 (PStDC3000), infection and their combination. Plants recovered from drought stress were also exposed to PStDC3000. Beside we have also infiltrated P. syringae pv tabaci (PSta, non-host pathogen) individually or in combination with drought stress. Using Affymetrix WT gene 1.0 ST array, global transcriptome profiling of plants leaves under individual drought stress and pathogen infection was compared with their combination. Results implicate that plants exposed to combined drought and pathogen stress experience a new state of stress where each combination of stressor and their timing defines the plant responses and thus should be studied explicitly. Global transcriptional analysis in Arabidopsis leaves exposed to individual and combined drought and pathogen stress.
2017-02-11 | GSE79681 | GEO
Project description:affy_popsec_nancy_stomata_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 laser-microdissected stomata, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. In response to water deficit, water loss is adjusted through stomatal conductance. Transcriptome of pure stomatal material should bring valuable information hardly reachable in whole leaf transcriptome analysis. 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.-Two poplar clones, Soligo (S) and Carpaccio (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. Five hundred stomata (one thousand five hundreds guard cells) were laser microdissected in mature leaves of each tree. Stomata from 3 trees (1500) were pooled for total RNAs extraction. A pool is considered as one biological replicate and corresponds to one Affymetrix slide. The two biological replicates originate from the same experiment. Keywords: treated vs untreated comparison
2013-02-28 | GSE17219 | GEO
Project description:affy_popsec_nancy_stomata_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 laser-microdissected stomata, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. In response to water deficit, water loss is adjusted through stomatal conductance. Transcriptome of pure stomatal material should bring valuable information hardly reachable in whole leaf transcriptome analysis. 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.-Two poplar clones, Soligo (S) and Carpaccio (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. Five hundred stomata (one thousand five hundreds guard cells) were laser microdissected in mature leaves of each tree. Stomata from 3 trees (1500) were pooled for total RNAs extraction. A pool is considered as one biological replicate and corresponds to one Affymetrix slide. The two biological replicates originate from the same experiment. Keywords: treated vs untreated comparison 16 arrays - poplar
2013-02-28 | E-GEOD-17219 | biostudies-arrayexpress
Project description:This was a comparative transcriptome analysis by using high throughput sequencing. To assess the effects of drought stress and NF-Y transcription factors ZmNF-YA1 and ZmNF-YB16 on maize, leaves from wild-type (W22), zmnf-ya1 (m67) mutant, wild-type (B104) and ZmNF-YB16 overexpression (OE) plants grow under well-watered and drought stress conditions were collected and RNAseq was performed. We tracked the gene expression events of inbred maize lines W22 or B104 seedlings in response to drought stress to evaluate how drought stress affects the gene expression program in maize. At the same time, we analyzed the effects of drought stress on gene expression in zmnf-ya1 and ZmNF-YB16 OE plants to investigate whether and how ZmNF-YA1 and ZmNF-YB16 confer drought stress tolerance in maize. Maize plants were grown under well-watered conditions until the V4 stage (zmnf-ya1 and W22) or V9 stage (ZmNF-YB16 OE and B104), and then half of them were exposed to drought stress treatment. Water loss in the soil and the electrolyte leakage from leaf cells were used to assess drought stress in plants. Leaves from 3-4 plants were pooled for each sample, and two replicates were used. RNA was extracted from small strips of leaf lamina excised from the first fully expanded leaf of the plants.
2019-09-21 | GSE137780 | GEO
Project description:affy_popsec_nancy_roots_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 root apices, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. 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. 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 better discriminate genes presenting a potential adaptative character from genes responding passively to the constraint.-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. Four to eight root apices (1 cm-long) were collected on each individual tree. Total RNAs were extracted from all roots for 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. The two biological replicates originate from the same experiment. Keywords: treated vs untreated comparison
2011-01-15 | GSE17223 | GEO
Project description:affy_popsec_nancy_roots_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 root apices, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. 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. 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 better discriminate genes presenting a potential adaptative character from genes responding passively to the constraint.-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. Four to eight root apices (1 cm-long) were collected on each individual tree. Total RNAs were extracted from all roots for 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. The two biological replicates originate from the same experiment. Keywords: treated vs untreated comparison 16 arrays - poplar
2011-01-15 | E-GEOD-17223 | biostudies-arrayexpress
Project description:The drought stress is one of key adverse environmental factors limiting plant growth and development, even threating global crop productivity in many arid and semi-arid regions. Drought stress usually causes huge economic losses for tobacco industries. Understanding how plants respond and adapt to the drought stress helps generate engineered plants with enhanced drought resistance. In this study, integrative analyses of multiple time point-related transcriptome and metabolome generated from K326 and its derived mutant 28 (M28) with contrasting drought tolerance. We found that dramatic changes of gene expression profiles between M28 and K326 before and after drought treatment.
2022-09-26 | GSE214048 | GEO