Functional genomic analysis of cold acclimation in the genus Solanum
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ABSTRACT:
ORGANISM(S): Solanum tuberosum
PROVIDER: GSE8281 | GEO | 2007/09/01
SECONDARY ACCESSION(S): PRJNA101239
REPOSITORIES: GEO
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Project description:Healthy five-weeks old S. tuberosum (Red Pontiac) and S. commersonii (Oka 5040) were subjected to cold-acclimating temperature (2oC) in the growth chamber. Control plants at identical developmental stage were also grown in growth chamber at optimum conditions for growth (28oC, 14/10, light/dark, 65% RH). Leaf tissues were collected from the control (reference) and cold-acclimating (experimental treatment, 2oC) plants for each species at 2, 4, 7, 10 and 14 days after the initiation of the control and low temperature treatments. A total of two plants for each species were used for both the control and treatment experiments and tissue samples from each plant (within replicate) were pooled for RNA isolation. These experiments were performed twice in order to produce two sets of biological replicates for each species for all sampling time-points. Keywords: Reference design 17 hybs total
2007-08-31 | E-GEOD-8281 | biostudies-arrayexpress
Project description:We investigated effect of severe cold to diurnal transcriptome changes in maize 3rd leaf. We used chilling-sensitive inbred line CM109. Kernels were germinated in wet sand in darkness at 25C. Seedlings were transferred to growth chamber (photoperiod 14/10h, temperature 24, light 250 umol quanta x m-2 x s-1). After full development of the third leaf (fully developed ligular region) plants were used for experiments. The experiment was begun at the start of the dark period (time zero), at which time a large sample (eight plants) was taken to serve as a reference in hybridizations. Half of the plants were transferred to cold chamber (day/night temperature 8/6°C, photoperiod 14/10 h, light 250 umol quanta•m-2•s-1) other half served as control (day/night temperature 24/22°C, other parameters was the same as for cold treatment). Further samples were taken after 200, 400, 600 (dark period) and 810, 1020, 1230, 1440 minutes (light period) of growth (total 24 hours). Each sample consisted of the middle part of the third leaf blade, pooled from three plants and frozen in liquid nitrogen. The experiment was replicated four times with two replications dye swapped.
2017-08-21 | E-MTAB-1252 | biostudies-arrayexpress
Project description:affy_sunflower_2011_02 - affy_sunflower_2011_02 - The early sowing constitutes an alternative strategy to avoid drought occurring during flowering and post-flowering periods and responsible for decrease in sunflower production. In French cropping system, early sowing is associated to low temperature period and frost during first development stages in sunflower. Knowledge about metabolism of frost acclimation must be performed to supply tools for breeding programs in sunflower. The aim of our experiment is to unravel the transcriptional regulation underpinning frost tolerance in sunflower-5 genotypes of sunflower were grown in a growth chamber 1 (23°C day/18°C night, 63% air humidity, 14 hours day photoperiod). At the stage of 6 leaves well-developed, 12 plants of each genotype were subjected to cold acclimation (+4°C during 2 days) in another growth chamber 2. Then, these plants were subjected to 2 nights at -3°C (frost treatment). Chlorophylle fluorescence, Osmotic potential, Relative electrolyte leakage were then determined in the following conditions : - 6th October on 6 plants X 5 genotypes from growth chamber 1 (C1) - 6th October on 6 plants X 5 genotypes from growth chamber 2 (S1) - 11th October on 6 plants X 5 genotypes from growth chamber 1 (C2) - 11th October on 6 plants X 5 genotypes from growth chamber 1 (S2)
2013-09-01 | GSE45586 | GEO
Project description:We investigated effect of severe cold on transcriptome changes in two inbred maize lines, chilling-sensitive ETH-DL3 and chilling-tolerant ETH-DH7. Kernels were germinated in wet sand in darkness at 25C. Seedlings were transferred to growth chamber (day/night temperature 24/22C, photoperiod 14/10 h, light 250 umol quanta x m-2 x s-1) and grow in pots containing Knop's nutrient solution supplemented with Hoagland's micro-nutrients. After full development of the 3rd leaf (fully developed ligular region) plants were used in experiment. The experiment was begun at the start of the dark period. Half of the plants were transferred to cold chamber (day/night temperature 8/6C, photoperiod 14/10 h, light 250 umol quanta x m-2 x s-1) other half served as control (day/night temperature 24/22C, other parameters was the same as for cold treatment). After dark period (10h) and 200 minutes of light period samples were taken. Each sample consisted of the middle part of the 3rd leaf blade, pooled from three plants and frozen in liquid nitrogen. The experiment was replicated four times with two replications dye swapped.
2014-03-15 | E-MTAB-1315 | biostudies-arrayexpress
Project description:Functions of Arabidopsis REI1-LIKE (REIL) proteins, two homologs of a yeast ribosome biogenesis protein (RBP) that takes part in the late cytoplasmic steps of 60S ribosomal subunit maturation, were characterized by systems analyses of the 10°C cold acclimating reil1-1 reil2-1 double mutant compared to Col-0 wildtype. The mutant lacked both REIL proteins, was strongly growth inhibited in the cold and complemented by constitutive expression of N-terminal FLUORESCENT PROTEIN (FP)-REIL1 and FP-REIL2 fusion proteins under control of the UBIQUITIN 10 promoter. Wildtype acclimation to 10°C causes relative accumulation of cytosolic ribosome subunits and rRNA. Expression of cytosolic ribosomal genes, known cytosolic RBPs, translation initiation- and elongation-factors was activated. Conserved function of Arabidopsis REIL proteins was indicated by delay of these processes in reil1-1 reil2-1, cytosolic localization of FP-REIL proteins and native REIL protein interactions with 60S containing ribosome fractions. Non-acclimated reil1-1 reil2-1 triggered plant specific metabolic and transcriptomic cold acclimation responses that included activation of the DREB/CBF-regulon with a preference for the cold acclimation factors, CBF1/DREB1B, CBF2/DREB1C, and CBF3/DREB1A. Cold-acclimating reil1-1 reil2-1 maintained cellular integrity and acquired freezing tolerance but did not activate FLOWERING LOCUS T expression in mature leaves. This block was independent of FLOWERING LOCUS C and AGAMOUS-LIKE 19 mediated vernalization. We conclude that Arabidopsis REIL proteins enhance accumulation of cytosolic ribosome subunits after cold shift and either directly or indirectly feedback on temperature perception by suppression of premature cold acclimation at optimized temperature and by triggering growth and the vegetative to generative phase transition in the cold. Transcriptomic profiling demonstrated a hidden acclimation phenotype of the morphologically inconspicuous reil1-1reil2-1 mutant under optimized temperature conditions. Premature triggering of cold acclimation, a severe growth defect at 10°C and compensation responses indicate that REIL function may extend beyond cytosolic ribosome biogenesis towards translation initiation.
2018-02-01 | GSE101111 | GEO
Project description:affy_sunflower_2011_02 - affy_sunflower_2011_02 - The early sowing constitutes an alternative strategy to avoid drought occurring during flowering and post-flowering periods and responsible for decrease in sunflower production. In French cropping system, early sowing is associated to low temperature period and frost during first development stages in sunflower. Knowledge about metabolism of frost acclimation must be performed to supply tools for breeding programs in sunflower. The aim of our experiment is to unravel the transcriptional regulation underpinning frost tolerance in sunflower-5 genotypes of sunflower were grown in a growth chamber 1 (23°C day/18°C night, 63% air humidity, 14 hours day photoperiod). At the stage of 6 leaves well-developed, 12 plants of each genotype were subjected to cold acclimation (+4°C during 2 days) in another growth chamber 2. Then, these plants were subjected to 2 nights at -3°C (frost treatment). Chlorophylle fluorescence, Osmotic potential, Relative electrolyte leakage were then determined in the following conditions : - 6th October on 6 plants X 5 genotypes from growth chamber 1 (C1) - 6th October on 6 plants X 5 genotypes from growth chamber 2 (S1) - 11th October on 6 plants X 5 genotypes from growth chamber 1 (C2) - 11th October on 6 plants X 5 genotypes from growth chamber 1 (S2) 12 arrays - SUNFLOWER; treated vs untreated comparison
2013-09-01 | E-GEOD-45586 | biostudies-arrayexpress
Project description:To investigate the temperature response in Thermosynechococcus elongatus (BP-1) and look for coordinated control in the cell, transcriptomes of BP-1 were measured using RNAseq following exposure to low and high temperature stress. The amount of temperature increase (53 to 61 °C) and decrease (53 to 45 °C) was based on the allowable range of continuous growth. The cells were growth in three separate culture tubes under LED light in a temperature-controlled submersible chamber under batch growth conditions. The temperature shift was conducted once the cells reached their target concentration of 1.5E7 cells/ml. A control experiment was conducted, in which the temperature remained at 53 °C, ensuring that the cellular physiology and light attenuation were comparable and that the only difference between the hot and cold treatments relative to the control treatment was temperature.
2015-06-22 | GSE70086 | GEO
Project description:12plex_vitis_2012_04 - cold stress - In temperate species, low temperatures adversely affect plant growth and development, constraining spatial expansion and productivity. Cold can trigger adaptive process or lead to alterations in physiological traits when stress intensity exceeds a certain threshold. Grapevine flower development and fruit set are influenced by cold nights in the vineyard. The correct formation of sexual organs and the success of reproduction are dependent upon sugar supply which can be affected by low temperatures. Many pathways of carbon metabolism may be affected by low temperatures however limited information is available about fluctuations in carbon metabolism in inflorescences. - Experiments were performed on inflorescence of Vitis vinifera L. cv. Pinot noir fruiting cuttings. First, inflorescences at female meiosis were collected the day of the experiment, then cuttings with the inflorescence were placed at 0°C for a 8 h night. Control plants were maintained in a growth chamber for 8 h at 19°C. Inflorescences were collected after 1 h and 8 h of cold. Additional time point was performed 2 h after the end of the cold night by placing the inflorescence at 25°C after the end of the cold night. Control plants were also collected.
2016-10-01 | GSE87296 | GEO
Project description:Eighteen genetically-diverse maize hybrids (Zea mays, dent lines crossed to a flint inbred-line) were cultivated in a growth-chamber at optimal temperature (20°C) for three weeks. They were then submitted to three successive steps of decreasing temperature ( 16, 13 and 8.5°C). Each step lasted two days. Samples were taken on the youngest ligulated leaf (fourth or fifth leaf) at the end of the period at 20°C and at the end of each temperature step. Three replicates per genotype/ temperature combination were analyzed. Each replicate was made up of the mix of leaf samples from different plants.
2021-01-19 | PXD021790 | Pride
Project description:During low temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. During deacclimation in response to warm temperatures cold acclimated plants lose freezing tolerance and resume growth and development. While considerable effort has been directed toward understanding the molecular and metabolic basis of cold acclimation, much less information is available about the regulation of deacclimation. Here, we report metabolic (GC-MS) and transcriptional (microarrays, qRT-PCR) responses underlying deacclimation during the first 24 h after a shift of cold acclimated Arabidopsis thaliana (Columbia-0) plants to warm temperature. The data revealed a faster response of the transcriptome than of the metabolome and provided evidence for tightly regulated temporal responses at both levels. Metabolically deacclimation is associated with decreasing contents of sugars, amino acids and glycolytic and TCA cycle intermediates, indicating an increased need for carbon sources and respiratory energy production associated with growth resumption under warm temperature conditions. Deacclimation also involves extensive down-regulation of protein synthesis and changes in the metabolism of lipids and cell wall components. Altered hormonal regulation appears particularly important during deacclimation, with changes in the expression of genes related to auxin, gibberellin, brassinosteroid, jasmonate and ethylene metabolisms. Several transcription factor families controlling fundamental aspects of plant development are significantly regulated during deacclimation, emphasizing that loss of freezing tolerance and growth resumption are interrelated processes that are transcriptionally highly interrelated. Expression patterns of some clock oscillator components during deacclimation resembled those under warm conditions, indicating at least partial re-activation of the circadian clock. This study provide the first comprehensive analysis of the regulation of deacclimation in cold acclimated plants. The data indicate cascades of rapidly regulated genes and metabolites that underly the developmental switch resulting in reduced freezing tolerance and the resumption of growth. They constitute a reference dataset of genes, metabolites and pathways that are crucial during the first rapid phase of deacclimation and will be useful for the further analysis of this important but under-researched plant process. We used whole genome microarrays to monitor changes in gene expression in the Arabidopsis thaliana accession Columbia-0 during the first 24 h after a shift of cold acclimated plants to warm temperature.
2017-09-18 | GSE86935 | GEO