Arabidopsis Me-0 vs tetraploid Col
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE71914 | GEO | 2016/01/14
SECONDARY ACCESSION(S): PRJNA292444
REPOSITORIES: GEO
Similar Datasets
Project description:To investigate gene expression differences related to the regulation of stomatal aperture between two Arabidopsis accessions, Me-0 and tetraploid Col, we performed microarray analysis on guard cell protoplasts from these two accessions. We identified 1,777 probes as up-regulated and 1,706 probes as down-regulated differentially expressed genes (DEGs) in Me-0 compared with tetraploid Col (adjusted P-value < 0.001 and log 2 fold change of greater than 1 or less than -1). Using gene set analysis to functionally characterize DEGs, there were eight significant gene sets (at the level of P-value < 0.01) among the up-regulated genes and seven significant gene set among the down-regulated genes. Genes with the lowest P-value among the up-regulated genes were related to âplant-type cell wall looseningâ, an essential step in guard cell swelling. Most of the down-regulated genes were related to the defense responses for immunity, hypoxia, and ozone, which also influence stomatal responses or gas exchange. We propose that these gene expression differences may cause the difference in stomatal aperture between Me-0 and tetraploid Col. Four samples from Me-0 and three samples from tetraploid Col are used for a microarray analysis.
2016-01-14 | E-GEOD-71914 | biostudies-arrayexpress
Project description:Stomata are highly specialized organs which consist of pairs of guard cells and regulate gas and water vapor exchange in plants. While early stages of guard cell differentiation have been described and were interpreted in analogy to processes of cell type differentiation in animals, the downstream development of functional stomatal guard cells remains poorly understood. We have isolated an Arabidopsis mutant, scap1 (stomatal carpenter 1), that develops irregularly shaped guard cells and lacks the ability to control stomatal aperture, including CO2-induced stomatal closing and light-induced stomatal opening. SCAP1 was identified as a plant-specific Dof-type transcription factor expressed in maturing guard cells but not in guard mother cells. SCAP1 regulates the expression of genes encoding key elements of stomatal functioning and morphogenesis, such as a K+ channel protein, MYB60 transcription factor, and pectin methyl esterase. Consequently, ion homeostasis was disturbed in scap1 guard cells, and esterification of extracellular pectins was impaired so that the cell walls lining the pores did not mature normally. We conclude that SCAP1 regulates essential processes of stomatal guard cell maturation and functions as a key transcription factor regulating the final stages of guard cell differentiation. We isolated guard cell protoplasts from 4-week-old WT(Col-0) and scap1 mutant plants and extracted RNA independently. Four biological replicates were performed for each experiment.
2013-02-28 | E-GEOD-43964 | biostudies-arrayexpress
Project description:Stomata are highly specialized organs which consist of pairs of guard cells and regulate gas and water vapor exchange in plants. While early stages of guard cell differentiation have been described and were interpreted in analogy to processes of cell type differentiation in animals, the downstream development of functional stomatal guard cells remains poorly understood. We have isolated an Arabidopsis mutant, scap1 (stomatal carpenter 1), that develops irregularly shaped guard cells and lacks the ability to control stomatal aperture, including CO2-induced stomatal closing and light-induced stomatal opening. SCAP1 was identified as a plant-specific Dof-type transcription factor expressed in maturing guard cells but not in guard mother cells. SCAP1 regulates the expression of genes encoding key elements of stomatal functioning and morphogenesis, such as a K+ channel protein, MYB60 transcription factor, and pectin methyl esterase. Consequently, ion homeostasis was disturbed in scap1 guard cells, and esterification of extracellular pectins was impaired so that the cell walls lining the pores did not mature normally. We conclude that SCAP1 regulates essential processes of stomatal guard cell maturation and functions as a key transcription factor regulating the final stages of guard cell differentiation.
2013-02-28 | GSE43964 | GEO
Project description:The aim of this study was to analyze the impact of autotetraploidy on gene expression in Arabidopsis thaliana by comparing diploid versus tetraploid transcriptomes. In particular, this included the comparison of the transcriptome of different tetraploid A. thaliana ecotypes (Col-0 vs. Ler-0). The study was extended to address further aspects. One was the comparison of the transcriptomes in subsequent generations. This intended to obtain information on the genome wide stability of autotetraploid gene expression. Another line of work compared the transcriptomes of different diploid vs. tetraploid tissues. This aimed to investigate whether particular gene groups are specifically affected during the development of A. thaliana autotetraploids. Samples 1-8: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 9-12: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 13-24: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 25-32: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 33-36: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Ler-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 37-40: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Col-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 41-44: Arabidopsis thaliana Col-0/Ler-0 diploid transcriptome. Transcriptional profiling and comparison of diploid Col-0 vs. diploid Ler-0 seedlings. The experiment was carried out with pedigree of esrablished lines. Samples 45-48: Arabidopsis thaliana Col-0/Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid Col-0 vs tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 and Ler-0 lines.
2010-05-01 | GSE18482 | GEO
Project description:Abscisic acid (ABA) is a key hormone for plant growth, development and stress adaptation. Perception of ABA through four types of receptors has been reported. We show here that impairment of ABA perception through the PYR/PYL/RCAR branch reduces vegetative growth and seed production, and leads to a severely open stomata and dramatic ABA insensitive phenotype, even though other branches for ABA perception remain functional. Arabidopsis sextuple mutant impaired in 6 PYR/PYL receptors, namely PYR1, PYL1, PYL2, PYL4, PYL5 and PYL8, was able to germinate and grow even on 100 mM ABA. Whole-rosette stomatal conductance (Gst) measurements revealed that leaf transpiration in the sextuple pyr/pyl mutant was higher than in the ABA-deficient aba3-1 or ABA-insensitive snrk2.6 mutants. The gradually increasing Gst values of plants lacking three, four, five and six PYR/PYLs indicate quantitative regulation of stomatal aperture by this family of receptors. The sextuple mutant lacked ABA-mediated activation of SnRK2s and ABA-responsive gene expression was dramatically impaired as was reported in snrk2.2/2.3/2.6. In summary, these results show that ABA perception by PYR/PYLs plays a major role to regulate seed germination and establishment, basal ABA signaling required for vegetative and reproductive growth, stomatal aperture and transcriptional response to the hormone. Four biological replicates were generated for the 3 genotypes, pyr1pyl1pyl2pyl4pyl5pyl8 sextuple mutant, snrk2.2/2.3/2.6 triple mutant, and Col-0. All the samples were treated with ABA for 3 hours before harvesting. The four Col-0 samples were mix to create an unique reference Col-0 sample. Two comparasion were made, fisrt one, PYR/PYL sextuple mutant versus Col-0 reference sample and second one, SnRK2 triple mutant versus Col-0 reference sample. In each comparasion four biological replicates were made. Replicas number 1 and 2 were labeled with Cy5 for the mutant sample and Cy3 for the Col-0 reference sample, while the other two replicas,#3 and #4, were reversed-labeled.
2012-11-30 | E-GEOD-36692 | biostudies-arrayexpress
Project description:Flavonols are a class of flavonoids. Unlike other classes of flavonoids, flavonols strongly accumulate in guard cells, but the role of their accumulation in guard cells is still unclear so far.The overexpression of TaFLS1, a flavonol synthase gene from wheat, improves flavonol content in guard cells of Arabidopsis, while the mutant fls1-3 of Arabidopsis AtFLS1 reduces the content. Both the increase of flavonols by TaFLS1 overexpression and the decrease in fls1-3 change stomatal apeture, showing the association between flavonols and stomatal movements. We used microarrays to detail the global programme of gene expression underlying both the increase and decrease of flavonol content and identified possible mechanism of flavonols-mediated stomatal movement. Arabidipsis Col-0, TaFLS1 overexpression lines, and fls1-3 were used for analysis. Leaves of six-week old Arabidopsis seedlings grown in soils under the regime of a 16 h photoperiod at 22°C and 60% relative humidity were sampled, and RNA was extracted for microarray analysis. Each of Arabidopsis lines has three replicates.
2014-02-01 | E-GEOD-54593 | biostudies-arrayexpress
Project description:To identify genes of the guard cell transcriptome of Arabidopsis thaliana enriched guard cell samples were compared with total leaf tissue. Genes of the abscisic acid and humidity response of Arabidopsis thaliana guard cells were identified by treatment with ABA-Spray and low humidity. total samples analysed are 24: 4 biological independent replicates of: total leaf (COL-0) vs. enriched guard cells (COL-0); ABA-sprayed enriched guard cells (gl1-1) vs. control-sprayed enriched guard cells (gl1-1); low humidity (20%rh) treated enriched guard cells (COL-0) vs. high humidity (80%) treated enriched guard cells (COL-0)
2013-01-14 | E-GEOD-41054 | biostudies-arrayexpress
Project description:We previously showed that increased levels of the tomato DELLA protein PROCERA (PRO) promoted ABA responses in guard cells, including ABA-induced stomatal closure and gene expression. Thus we aimed to identifiy DELLA-regulated genes in guard cells in order to study the molecular mechanism by which DELLA promotes stomatal closure.
2021-09-09 | GSE143999 | GEO
Project description:Drought and salt stress severely inhibit plant growth and development. However, the regulatory mechanisms of plants in response to these stresses are not fully understood. Here we find that the expression of a WRKY transcription factor WRKY46 is rapidly induced by drought, salt and oxidative stresses. Mutations of WRKY46 by T-DNA insertion lead to more sensitive to drought and salt stress, whereas, overexpression of WRKY46 exhibits hypersensitive in soil culture with higher water loss rate, but increased tolerance on the agar plates. ABA induced stomatal closing is impaired in the WRKY46 overexpressing line (OV46), which is potentially due to the lower ROS accumulation in the guard cells. Real-time qPCR and GUS activity assay further demonstrate that WRKY46 is expressed in guard cells, but its expression is not affected by dehydration treatment, suggesting different regulatory mechanisms for WRKY46 between guard cells and other WRKY46 expressed tissues. The stomatal movement and conductance assay indicate that WRKY46 is involved in light-dependent stomatal opening. Further microarray analysis reveals that WRKY46 regulates a set of genes involved in cellular osmoprotection and redox homeostasis under dehydration stress. Determinations of ROS and MDA content confirm its role in oxidative detoxification under stress. Furthermore, we find that WRKY46 modulates light-dependent starch metabolism in guard cells via regulating QQS gene expression. Taken together, we demonstrate that WRKY46 plays a role in modulating cellular osmoprotection and redox homeostasis under drought and salt stress, and functions independently in stomatal movement via regulating light-dependent starch metabolism and ROS levels in guard cells. We used microarrays to identify the certain downstream genes regulated by WRKY46 under normal and dehydration conditions. One-week-old Arabidopsis seedlings of wild-type Col-0 (WT) and WRKY46 overexpressing line (46T) with or without dehydration treatment for 1 h were harvested and used for RNA extraction and hybridization to Affymetrix Arabidopsis ATH1 microarrays. The experiment includes 3 biological replicates.
2015-02-01 | E-GEOD-49418 | biostudies-arrayexpress
Project description:a2e_heterosis - cgh_colvscvi_wg - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and CVi.
2011-05-17 | GSE24835 | GEO