Dynamics of leaf transcriptome during cold acclimation in wheat
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA657302 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12455744_1.fastq.gz | Fastqsanger.gz | |||
| SRR12455744_2.fastq.gz | Fastqsanger.gz | |||
| SRR12455745_1.fastq.gz | Fastqsanger.gz | |||
| SRR12455745_2.fastq.gz | Fastqsanger.gz | |||
| SRR12455746_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 44 |
Similar Datasets
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
2022-10-24 | GSE156300 | GEO
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.
2014-10-10 | GSE61621 | 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: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. Expression patterns were compared between a synthetic wheat line which treated 24M-bM-^DM-^C and 4M-bM-^DM-^C. Total RNA samples were respectively isolated from leaves and crown tissues of the synthetic line grown at normal temperature for 3 weeks and then at 4M-BM-0C for 12 and 6 weeks. Two independent experiments were conducted in each exprement.
2014-10-10 | E-GEOD-61621 | biostudies-arrayexpress
Project description:Different wheat cultivars may be classified as either winter or spring varieties depending on whether they require exposure to an extended period of cold in order to become competent to flower. Using a growth regime that mimics the conditions that occur during a typical winter in Britain, we wished to survey the genes that are involved in phase transition as well as those involved in cold-acclimation. Keywords: Time course
2008-10-01 | GSE11774 | GEO
Project description:Different wheat cultivars may be classified as either winter or spring varieties depending on whether they require exposure to an extended period of cold in order to become competent to flower. Using a growth regime that mimics the conditions that occur during a typical winter in Britain, we wished to survey the genes that are involved in phase transition as well as those involved in cold-acclimation. Experiment Overall Design: We wished to study the profiles of expression of genes involved in both phase transition (vegetative to reproductive growth transition) and cold-acclimation. To that end we we exposed plants to a gradual, stepped decline in both temperature and light. We sampled plants at three time points (3 weeks post-germination, 5 weeks post germination and 9 weeks post germination). We took samples from two separate tissues (crown and leaf) to se whether responses were different. We used two biological reps for each time point and tissue. Control plants were exposed to a delined in day-length and light intensity, but not in temperature.
2008-10-26 | E-GEOD-11774 | biostudies-arrayexpress
Project description:Experiment was designed to identify transcriptome changes during cold acclimation of Drosophila melanogaster male flies. Resistance to cold is often measured by recovery times from chill coma, which is induced almost immediately upon exposure to low but non-freezing temperatures (~0C), with flies becoming immobilised and losing motor activity. This paralysis is also ostensibly reversible upon return to normal temperatures, although again there can be longer term effects. Acclimation for increased cold resistance requires exposure periods ranging from hours or days to several weeks at low temperatures between 0C to 12C, and samples were taken during the cold acclimation period (1 hr, 2 hr, 3 hr, 6 hr, 12 hr, 24 hr, 36 hr and 48 hr).
2014-05-01 | E-MTAB-1607 | biostudies-arrayexpress
Project description:To understand physiological mechanisms of cold acclimation in pea, we performed a transcriptomique analysis in order to compare the response to LT treatment in two varieties, one being cold tolerant (Champagne) and the other cold sensitive (Terese).
2010-04-01 | GSE19209 | GEO
Project description:Differential gene expression during cold-acclimation in barley, wheat and rye
| PRJNA208239 | ENA
Project description:Two azide mutagenized lines Freeze Resistance (FR, 75% survival) and Freeze Susceptible (FS, 30% survival) were compared with and without 4°C ± 1.5 cold acclimation of crown tissue to identify genes responsible for the difference in freeze resistance. Keywords: Wheat cold acclimation, stress response, cold, low temperature
2013-07-01 | GSE14697 | GEO