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Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature

ABSTRACT: Five SAGE libraries were generated from A. thaliana leaf tissue collected at time points ranging from 30 minutes to one week of low temperature treatment (4°C). Over 240,000 high quality SAGE tags, corresponding to 16,629 annotated genes, provided a comprehensive survey of changes in the transcriptome in response to low temperature, from perception of the stress to acquisition of freezing tolerance. Keywords: SAGE; time course; stress response; cold acclimation; freezing tolerance

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE11461 | GEO | 2008/10/01

SECONDARY ACCESSION(S): PRJNA106377

REPOSITORIES: GEO

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Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature

Project description:Five SAGE libraries were generated from A. thaliana leaf tissue collected at time points ranging from 30 minutes to one week of low temperature treatment (4°C). Over 240,000 high quality SAGE tags, corresponding to 16,629 annotated genes, provided a comprehensive survey of changes in the transcriptome in response to low temperature, from perception of the stress to acquisition of freezing tolerance. Keywords: SAGE; time course; stress response; cold acclimation; freezing tolerance SAGE libraries were generated from A. thaliana leaf tissue collected after exposure to low temperature (4°C) for 0 minutes, 30 minutes, 2 hours, 2 days and one week, the tags were matched to the Arabidopsis genome and statistical analysis was performed to reveal differential gene expression.

2008-10-01 | E-GEOD-11461 | biostudies-arrayexpress

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Project description:Oil rapeseed (Brassica napus L.) is a typical winter biennial plant, with high cold tolerance during vegetative stage. In recent years, more and more early-maturing rapeseed varieties were planted across China. Unfortunately, the early-maturing rapeseed varieties with low cold tolerance have higher risk of freeze injury in cold winter and spring. Little is known about the molecular mechanisms for coping with different low-temperature stress conditions in rapeseed. In this study, we investigated 47,328 differentially expressed genes (DEGs) of two early-maturing rapeseed varieties with different cold tolerance treated with cold shock at chilling (4°C) and freezing (−4°C) temperatures, as well as chilling and freezing stress following cold acclimation or control conditions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that two conserved (the primary metabolism and plant hormone signal transduction) and two novel (plant-pathogen interaction pathway and circadian rhythms pathway) signaling pathways were significantly enriched with differentially-expressed transcripts. Our results provided a foundation for understanding the low-temperature stress response mechanisms of rapeseed. We also propose new ideas and candidate genes for genetic improvement of rapeseed tolerance to cold stresses.

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Project description:The crown is the critical region for survival of winter wheat exposed to low temperature stresses. When wheat is exposed to non-freezing low temperatures, they can increase their freezing tolerance (cold acclimation, ACC). Changes within the apoplast are thought to be crucial for acquisition of freezing tolerance. However, how individual tissues within the ccrown, namely the shoot apical meristem (SAM, responsible for new shoot growth) and vascular transition zone (VTZ, located at the base of the crown)enhance tolerance to freezing has not yet been characterized. In the present study, we conducted shotgun proteomic analysis of the apoplast fluid to investigate ACC-induced proteins in the SAM and VTZ.

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Gene expression profiles during long-term low-temperature treatment and cold acclimation in synthetic wheat hexaploids

Project description:We conducted microarray analysis to study comprehensive changes of gene expression profile under long-term low-temperature (LT) treatment and to identify other LT-responsive genes related with cold acclimation in seedling leaves and crown tissues (shoots containing apical meristems) of a synthetic hexaploid wheat line. The microarray analysis revealed marked up-regulation of a number of Cor/Lea genes and fructan biosynthesis-related genes under the long-term LT treatment. For validation of the microarray data, we selected four synthetic wheat lines, which contained the A and B genomes from a tetraploid wheat cultivar Langdon and the diverse D genomes originating from the different Ae. tauschii accessions, with distinct levels of freezing tolerance after cold acclimation. Quantitative RT-PCR analyses showed that the transcription accumulated levels of the Cor/Lea, CBF, and fructan biosynthesis-related genes were higher in more freezing-tolerant lines than those in the sensitive lines. The fructan biosynthesis pathway would be associated with cold acclimation to develop wheat freezing tolerance and related with diversity of the freezing tolerance level in addition to the CBF-mediated Cor/Lea expression pathway.

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RNA-SEQ of wheat Jing411

Project description:Exposure to cold conditions is a major abiotic stress affecting crop growth and productivity. Elucidation of genetic mechanisms underlying response to low temperature is needed. To assess the relationship between the genes and the cold tolerance of wheat, transcriptomics analyses were performed to study changes in gene profiles of cultivar Jing 411 after cold acclimation and freezing treatment. The wheat cultivar Jing 411 was subjected to transcriptome sequencing. The RNA was sequenced on a HiSeq 2500 platform, and the generated data were analyzed using TopHat v2.0.

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Cold acclimation process under limited light conditions in Arabidopsis thaliana

Project description:Plants in temperate regions have evolved mechanisms to survive sudden temperature drops. Previous reports have indicated that the cold acclimation mechanism is light-dependent and does not fully operate under a low light intensity. In these studies, plants were grown under a long-day photoperiod and were more sensitive to freezing stress. However, winter annuals like Arabidopsis thaliana Col-0 germinate in the fall, overwinter as rosettes, and therefore must acclimate under short photoperiods and low irradiance. The role of light intensity was analysed in plants grown under a short-day photoperiod at the growth stage 1.14. Plants were acclimated at 4 °C for seven days under 100 and 20 μmol m-2s-1 PPFD for control and limited-light conditions, respectively. All cold acclimated plants accumulated molecular markers reportedly associated with acquired freezing tolerance, including proline, sucrose, CBFs, and COR gene protein products dehydrins and low-temperature-responsive proteins LTIs. Observed changes indicated that low PPFD did not inhibit the cold acclimation process, and the freezing stress experiment confirmed similar survival rates. The molecular analysis found distinct PPFD-specific adaptation mechanisms that were manifested in contrasting content of anthocyanins, cytokinin conjugates, abundances of proteins forming photosystems, and enzymes of protein, energy, and ROS metabolism pathways. Finally, this study led to the identification of putative proteins and metabolite markers correlating with susceptibility to freezing stress of non-acclimated plants grown under low PPFD. Our data show that Arabidopsis plants grown under short-day photoperiod can be fully cold-acclimated under limited light conditions, employing standard and PPFD-specific pathways.

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Gene expression profiles during long-term low-temperature treatment and cold acclimation in synthetic wheat hexaploids

2014-10-10 | E-GEOD-61621 | biostudies-arrayexpress

Potential role of natural variation in the Arabidopsis CBF Pathway contributing to local adaptation of ecotypes collected from Italy and Sweden

Project description:The two Arabidopsis ecotypes that are adapted to Italy and Sweden, respectively, showed different degree of freezing tolerance. By comparing the low temperature transcriptomes of the IT and SW ecotypes, we showed CBF pathway plays a significant role in natural variation of freezing tolerance.

2015-12-30 | GSE67332 | GEO

SAGE

Project description:SAGE

| PRJNA75661 | ENA

Potential role of the CBF Pathway contributing to local adaptation of ecotypes collected from Italy and Sweden

Project description:The two Arabidopsis ecotypes that are adapted to Italy and Sweden, respectively, showed different degree of freezing tolerance. By comparing the low temperature transcriptomes of the IT and SW ecotypes with the CBF pathway being knocked out, we showed the CBF pathway plays a significant role in natural variation of freezing tolerance.

2018-07-30 | GSE106284 | GEO

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