Cold acclimation in rice
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB75953 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14104410.fastq.gz | Fastqsanger.gz | |||
| ERR14104411.fastq.gz | Fastqsanger.gz | |||
| ERR14104412.fastq.gz | Fastqsanger.gz | |||
| ERR14104413.fastq.gz | Fastqsanger.gz | |||
| ERR14104414.fastq.gz | Fastqsanger.gz |
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Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.
2014-10-15 | GSE57895 | GEO
Project description:Frost is a major abiotic stress limiting plant growth and development. Climate change models predict an increase in the magnitude and frequency of late-frost events, which, together with an observed loss of soil insulation, will significantly damage roots. To withstand freezing stress, plants have evolved an adaptative process known as cold acclimation. While this process is well documented, it is known that the plant response to multiple stresses is unique and cannot be deduced from the response to each stress taken separately. Here, we investigate the impact of long-term metal exposure on the cold acclimation of Salix viminalis roots. To do so, we used physiological, transcriptomic and proteomic approaches. We found that while metal exposure significantly affected plants morphology and physiology, it did not impede cold acclimation. The impact of the simultaneous exposure to metals and cold acclimation on the transcriptome was unique, while at the proteomic level, the cold acclimation component seemed to be dominant. Further analysis revealed that metals strongly and negatively impacted the cellular antioxidant system. While this should have led to a loss of frost tolerance, it was not observed. A group of proteins was identified that could have played a role in compensating the impediment of the antioxidative system in metal-exposed roots.
2024-02-14 | GSE218490 | GEO
Project description:Earlier findings indicated that light plays a critical role in the development of frost tolerance in winter cereals. However, the exact mechanism is still poorly understood. In the present work the effects of light during the cold acclimation period were studied in chilling-sensitive maize plants. The results show that although exposure to relatively high light intensities during cold acclimation at 15 °C causes various stress symptoms, it enhances the effectiveness of acclimation to chilling conditions (5 °C in the light). Interestingly, certain stress responses were light-dependent not only in the leaves, but also in the roots. A microarray study was also conducted to achieve a better understanding of the interaction of low temperature and light intensity during the cold hardening period. Numerous genes significantly differentially expressed were observed in almost all assimilation and metabolic pathways. Acclimation at moderately low temperature and low light intensity reduced the level of soluble sugars, while chilling increased it. Greater accumulation during hardening was detected at relatively high light intensity. It seems that the photoinhibition induced by low temperature is a necessary evil for cold acclimation processes in plants.
2020-12-31 | GSE107913 | GEO
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayM-oM-<M- v1. Control and treated biological replicates of cold-tolerant cultivar TNG67 (japonica) and cold-sensitive cultivar TCN1 (indica) were analyzed
2014-10-15 | E-GEOD-57895 | biostudies-arrayexpress
Project description:The experiment tested organ-specific responses of rice (Oryza sativa ssp. japonica) to cold stress with a special focus on phytohormonal regulation. Cold stress (5°C, 24 h) was applies on the whole plants, leaves or roots. The results showed distinct responses when cold stress was applied on leaves, relating to photosynthesis and sugar synthesis as well as specific changes in phytohormones. On the other hand, stress applied to roots was more similar to the stress on the whole plant indicating roots to be more important in cold stress responses. Acclimation by mild temperature (15°C, 12 h) highlighted changes which are connected even with lower temperature exposure or which are characteristic for untreated organs. Recovery (3 d) indicated ability of plants to restore growth which correlated between individual phytohormones and plant growth. The article connect transcriptome, hormonome, proteome and sugar analyses of rice cold-stress responses.
2024-01-01 | GSE246145 | GEO
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:MicroRNAs (miRNAs) play vital roles in various biological processes by leading to mRNA cleavage or translational repression, and are also involved in multiple stress conditions. However, the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study, high-throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control (28°C, 30 days) and cold-acclimation (18°C, 30 days) conditions. A total of 414 miRNAs, 349 known and 65 novel, were identified. Among those miRNAs, 24 (19 known and 5 novel) were up-regulated, and 23 (9 known and 14 novel) were down-regulated in cold acclimated cells. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses indicated that the known differentially expressed miRNAs (DE-miRNA) are involved in cold acclimation by regulation of phosphorylation, cell junction, intracellular signal transduction, ECM-receptor interaction and so on. Moreover, dre-miR-100-3p inhibitor or dre-miR-16b mimics could protect ZF4 cells under cold stress, indicating the involvement of miRNA in cold acclimation. In summary, the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation.
2019-12-17 | GSE134399 | GEO
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: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:For many organisms the ability to cold acclimate with the onset of seasonal cold has major implications for their fitness. In insects, where this ability is widespread, the physiological changes associated with increased cold tolerance have been well studied. Despite this, little work has been done to trace changes in gene expression during cold acclimation that lead to an increase in cold tolerance. We used an RNA-Seq approach to investigate this in two species of the Drosophila virilis group. We found that the majority of genes that are differentially expressed during cold acclimation differ between the two species. Despite this, the biological processes associated with the differentially expressed genes were broadly similar in the two species. These included: metabolism, cell membrane composition, and circadian rhythms, which are largely consistent with previous work on cold acclimation / cold tolerance. In addition, we also found evidence of the involvement of the rhodopsin pathway in cold acclimation, a pathway that has been recently linked to thermotaxis. Interestingly, we found no evidence of differential expression of stress genes implying that long-term cold acclimation and short-term stress response may have a different physiological basis.
2014-12-27 | GSE58925 | GEO