Transcriptome Analysis of Cold Acclimation in Barley Albina and Xantha Mutants1
Ontology highlight
ABSTRACT:
ORGANISM(S): Hordeum vulgare
PROVIDER: GSE10332 | GEO | 2009/04/29
SECONDARY ACCESSION(S): PRJNA108577
REPOSITORIES: GEO
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Project description:we investigated the transcriptome of barley albina and xantha mutants and the corresponding wild type to assess the effect of the chloroplast on expression of cold-regulated genes Experiment Overall Design: five barley genotypes with two treatments and three replicates were analysed
2009-05-11 | E-GEOD-10332 | biostudies-arrayexpress
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2014-12-31 | GSE47432 | GEO
Project description:The present transcript profiling compares the gene expression during cold-acclimation in different genotypes of barley (Hordeum vulgare L.), wheat (Triticum aestivum L.) and rye (Secale cereale L.) in order to determine factors influencing frost tolerance. Because of its outstanding robustness against adverse environmental conditions rye is considered to be a model species for abiotic stress tolerance. Wheat is moderate frost-tolerant and barley is most sensitive species in this study. The aim of this study elucidate conserved, as well as, species-specific gene regulation across the Triticeae. Furthermore, transcript abundances were correlated between the distinct frost tolerances of genotypes within each species in order to find candidate genes for frost tolerance.
2013-11-30 | GSE47882 | GEO
Project description:This dataset is associated with two publications 1. Elucidating the biochemical basis of trans-16:1 fatty acid change in leaves during cold acclimation in wheat. http://doi.org/10.1002/pei3.10044 In this study, comparative RNA-seq analyses with leaf tissues undergoing cold acclimation reveal concerted transcriptome shifts indicating a reduced chloroplast lipid pathway activity and increased cytosolic ER membrane lipid synthesis. To explore the underlying metabolic and transcriptional mechanisms responsible for the reduction of the t16:1 under cold, a detailed lipid analysis and comparative transcriptome study were conducted with four wheat cultivars during cold treatment. The RNA-seq dataset includes four wheat cultivars (Manitou, Winter Manitou, Norstar and Spring Norstar) treated with cold paired with control. The data as a whole show that leaf tissues experience a gradual decrease in chloroplast lipid pathway activity and the variation in the decline of chloroplast lipid synthesis in different cultivars manifest in the rate of decrease in t16:1decrease in leaf tissues. Future efforts are required to determine if and how the down regulation of the chloroplast lipid pathway is related to the development of winter hardiness. 2. Computational genomics insights into cold acclimation in wheat. https://doi.org/10.3389/fgene.2022.1015673 In this study, integrated computational approaches was employed to investigate the transcriptomics and lipidomics data associated with cold acclimation and vernalization in the four wheat genotypes of distinct cold tolerance. Differential expression was investigated between cold treated and control samples and between the winter-habit and spring-habit wheat genotypes. Collectively, 12,676 differentially expressed genes (DEGs) were identified. Principal component analysis of these DEGs indicated that the first, second, and third principal components (PC1, PC2, and PC3) explained the variance in cold treatment, vernalization and cold hardiness, respectively. Differential expression feature extraction (DEFE) analysis revealed that the winter-habit wheat genotype Norstar had high number of unique DEGs (1884 up and 672 down) and 63 winter-habit genes, which were clearly distinctive from the 64 spring-habit genes based on PC1, PC2 and PC3. Correlation analysis revealed 64 cold hardy genes and 39 anti-hardy genes. Cold acclimation encompasses a wide spectrum of biological processes and the involved genes work cohesively as revealed through network propagation and collective association strength of local subnetworks. Integration of transcriptome and lipidomics data revealed that the winter-habit genes, such as COR413-TM1, CIPKs and MYB20, together with the phosphatidylglycerol lipids, PG(34:3) and PG(36:6), played a pivotal role in cold acclimation and coordinated cohesively associated subnetworks to confer cold tolerance. Citations: http://doi.org/10.1002/pei3.10044 https://doi.org/10.3389/fgene.2022.1015673
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Project description:Plants due to their sessile nature rely on root systems to mediate many challenging stimuli. A major cornerstone of the responses are root proteomes, shaped to overcome biotic and abiotic cues. Proteome-wide reprogramming events are magnified in root meristems due to their active protein production. Using root meristems as a test system, we here study the major rewiring that plants face during cold acclimation. To achieve that, we performed tandem mass tag (TMT) label-mediated bottom-up proteomics of two consecutive segments of barley root apexes, comparing changes in global protein contents and individual protein abundances. We report an intricate translational reprogramming happening in the distal apex zone. The reprogramming includes all the translational machinery from ribosome biogenesis to protein folding, even suggesting roles for cold-specific ribosomal protein (RP) paralogs. Finally, this event is accompanied by upregulation of glutathione production and S-glutathionylation assemblage machineries. To summarize, we couple previous reports of an alternatively cold-spliced transcriptome to potential cold-specialized ribosomes and subsequent posttranslational modification (PTM), S-glutathione, of proteins. We propose that these PTMs protect the proteome during cold by acting as ROS scavengers, and consequently, provide a mechanistic link to the cold priming capabilities for root-specific biotic stress.
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Project description:Gene expression changes in a winter cultivar of barley in response to short and long term cold treatments ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Ben Trevaskis. The equivalent experiment is BB94 at PLEXdb.]
2011-03-08 | GSE27821 | GEO
Project description:Wild type Golden Promise barley and the frost tolerant TaCBF14 and TaCBF15 transgenic barley lines were grown in plant growth chamber in the Phytotron of ELKH ATK Agricultural Institute, Martonvasar, Hungary. After three weeks in control conditions, plants were treated by short-term cold-treatment. Samples were collected under control condition and after the short-term cold-treatment too.
2021-11-10 | E-MTAB-10781 | biostudies-arrayexpress
Project description:Differential gene expression during cold-acclimation in barley, wheat and rye
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Project description:Gene expression changes in a winter cultivar of barley in response to short and long term cold treatments ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Ben Trevaskis. The equivalent experiment is BB94 at PLEXdb.] treatment: Non-vernalized (3-replications); treatment: Short-term cold (3-replications); treatment: Vernalized (3-replications); treatment: 1 day post-vernalized (3-replications)
2011-03-08 | E-GEOD-27821 | biostudies-arrayexpress
Project description:In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Morex to low temperature, including triplicated measurements of cold, freeze/thaw cycles and de-acclimation over 33 days. Keywords: stress response
2008-02-02 | GSE6993 | GEO