RNA-seq of two early-maturing rapeseed varieties treated with different cold stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Brassica napus
PROVIDER: GSE129220 | GEO | 2020/03/19
REPOSITORIES: GEO
Similar Datasets
Project description:Our analysis of the sfr6 freezing-sensitive mutant (Knight, H., Veale, E., Warren, G. J. and Knight, M. R. (1999). Plant Cell 11, 875-886.) and cls8 (unpublished) chilling-sensitive mutant of Arabidopsis, has revealed that the expression of certain cold-regulated genes is aberrant in both these mutants. In order to understand the molecular basis of chilling and freezing stress in Arabidopsis and also to determine commonalities and differences between these 2 different physiological stress-tolerance processes, we request transcriptome analysis for both of these mutants compared to wild type in one experiment, upon cold treatment and at ambient conditions. The sfr6 mutant shows the most severe phenotype with respect to cold gene expression, but is tolerant to chilling (Knight, H., Veale, E., Warren, G. J. and Knight, M. R. (1999). Plant Cell 11, 875-886.). However, it is unable to cold acclimate and hence is sensitive to freezing. The cls8 mutant, on the other hand, has a relatively mild phenotype relative to the cold-regulated genes we have examined, but is very sensitive to chilling temperatures (15 to 10 degree centigrade). It is thus likely that in cls8 we have not yet identified the genes which are most affected, and which account for the physiological phenotype. Both sfr6 and cls8 have been fine-mapped and are close to being cloned. The cls8 mutant has an altered calcium signature in response to cold which means it is likely to be affected in early signalling, e.g. cold perception itself.We will compare the expression profiles of genes in sfr6, cls8 and Columbia (parental line for both mutants), both at ambient, and after treatment with cold (5 degrees) for 3 hours. This timepoint is designed to ÃÂcaptureÃÂ both rapidly responding genes e.g. CBF/DREB1 transcription factors, and also more slow genes e.g. COR genes (KIN1/2 and LTI78). Pilot northerns confirm that this time point is suitable.This analysis will provide new insight into 2 novel genes required for tolerance to low temperature in Arabidopsis, and additionally will determine the nature of overlap between the separate processes of chilling and freezing tolerance.
2022-11-21 | E-NASC-37 | biostudies-arrayexpress
Project description:Our analysis of the sfr6 freezing-sensitive mutant (Knight, H., Veale, E., Warren, G. J. and Knight, M. R. (1999). Plant Cell 11, 875-886.) and cls8 (unpublished) chilling-sensitive mutant of Arabidopsis, has revealed that the expression of certain cold-regulated genes is aberrant in both these mutants. In order to understand the molecular basis of chilling and freezing stress in Arabidopsis and also to determine commonalities and differences between these 2 different physiological stress-tolerance processes, we request transcriptome analysis for both of these mutants compared to wild type in one experiment, upon cold treatment and at ambient conditions. The sfr6 mutant shows the most severe phenotype with respect to cold gene expression, but is tolerant to chilling (Knight, H., Veale, E., Warren, G. J. and Knight, M. R. (1999). Plant Cell 11, 875-886.). However, it is unable to cold acclimate and hence is sensitive to freezing. The cls8 mutant, on the other hand, has a relatively mild phenotype relative to the cold-regulated genes we have examined, but is very sensitive to chilling temperatures (15 to 10 degree centigrade). It is thus likely that in cls8 we have not yet identified the genes which are most affected, and which account for the physiological phenotype. Both sfr6 and cls8 have been fine-mapped and are close to being cloned. The cls8 mutant has an altered calcium signature in response to cold which means it is likely to be affected in early signalling, e.g. cold perception itself.We will compare the expression profiles of genes in sfr6, cls8 and Columbia (parental line for both mutants), both at ambient, and after treatment with cold (5 degrees) for 3 hours. This timepoint is designed to Âcapture both rapidly responding genes e.g. CBF/DREB1 transcription factors, and also more slow genes e.g. COR genes (KIN1/2 and LTI78). Pilot northerns confirm that this time point is suitable.This analysis will provide new insight into 2 novel genes required for tolerance to low temperature in Arabidopsis, and additionally will determine the nature of overlap between the separate processes of chilling and freezing tolerance. Experiment Overall Design: Number of plants pooled:40-60
2008-06-14 | E-GEOD-6167 | biostudies-arrayexpress
Project description:Our analysis of the sfr6 freezing-sensitive mutant (Knight, H., Veale, E., Warren, G. J. and Knight, M. R. (1999). Plant Cell 11, 875-886.) and cls8 (unpublished) chilling-sensitive mutant of Arabidopsis, has revealed that the expression of certain cold-regulated genes is aberrant in both these mutants. In order to understand the molecular basis of chilling and freezing stress in Arabidopsis and also to determine commonalities and differences between these 2 different physiological stress-tolerance processes, we request transcriptome analysis for both of these mutants compared to wild type in one experiment, upon cold treatment and at ambient conditions. The sfr6 mutant shows the most severe phenotype with respect to cold gene expression, but is tolerant to chilling (Knight, H., Veale, E., Warren, G. J. and Knight, M. R. (1999). Plant Cell 11, 875-886.). However, it is unable to cold acclimate and hence is sensitive to freezing. The cls8 mutant, on the other hand, has a relatively mild phenotype relative to the cold-regulated genes we have examined, but is very sensitive to chilling temperatures (15 to 10 degree centigrade). It is thus likely that in cls8 we have not yet identified the genes which are most affected, and which account for the physiological phenotype. Both sfr6 and cls8 have been fine-mapped and are close to being cloned. The cls8 mutant has an altered calcium signature in response to cold which means it is likely to be affected in early signalling, e.g. cold perception itself.We will compare the expression profiles of genes in sfr6, cls8 and Columbia (parental line for both mutants), both at ambient, and after treatment with cold (5 degrees) for 3 hours. This timepoint is designed to capture both rapidly responding genes e.g. CBF/DREB1 transcription factors, and also more slow genes e.g. COR genes (KIN1/2 and LTI78). Pilot northerns confirm that this time point is suitable.This analysis will provide new insight into 2 novel genes required for tolerance to low temperature in Arabidopsis, and additionally will determine the nature of overlap between the separate processes of chilling and freezing tolerance. Keywords: strain_or_line_design
2007-01-22 | GSE6167 | GEO
Project description:Recently, intensive global climate change has become a major factor impacting plant survival during the winter. Freezing cold temperatures during the winter and abnormal temperature fluctuations during the winter and early spring are the most harmful ambient factors threatening tea plant winter survival and currently cause marked economic losses in tea production. In this study, by simulating natural climate change, we established cold acclimation (CA) and rapid cold stress (after CA) conditions to comprehensively investigate the transcriptome changes involved in CA and rapid cold stress. Electrolyte leakage (EL) rate and expression profile clustering analyses confirmed that the experimental design was valid. Comparative transcription analysis identified many differentially expressed genes (DEGs) involved in both processes. Time course and pathway enrichment analyses further revealed the physiological changes that occur during the initial period of CA and the cell wall changes that occur throughout the entire CA process; these changes play crucial roles in increasing freezing tolerance during this process. Compared with CA, different cold response mechanisms were rapidly activated under cold stress; however, the subsequent accumulation of reactive oxygen species, which affect multiple aspects, caused by freezing cold could be the harshest factor impairing tea leaves. Moreover, we investigated 60 DEGs shared by both processes and highlighted the importance of KCSs, HXXXD-type acyl-transferase family proteins, NAC080, SWEETs and ENOs in the responses to various cold conditions. These results greatly improve our knowledge of cold response mechanisms in tea plants and provide meaningful information for functional studies investigating cold tolerance-related genes.
2017-09-29 | GSE104390 | GEO
Project description:Chilling is a major stress to plants of subtropical and tropical origins including maize. To reveal molecular mechanisms underlying chilling tolerance and chilling survival, we investigated maize transcriptome responses to chilling stress in differentiated leaves and roots as well as in crowns with meristem activity for survival. Chilling stress on maize shoots and roots is found to each contribute to seedling lethality in maize. Comparison of maize lines with different chilling tolerance capacity reveals that chilling survival in maize is highly associated with upregulation in leaves and crowns of abscisic acid response pathway, transcriptional regulators and cold response as well as downregulation of heat response in crowns. Comparison of chilling treatment on whole and part of the plants reveals that response to distal-chilling is very distinct from, and sometimes opposite to, response to local- or whole-plant chilling in both leaves and roots, suggesting a communication between shoots and roots in environmental perception. In sum, this study details chilling responses in leaves, roots and crowns and reveals potential chilling survival mechanism in maize, which lays ground for further understanding survival and tolerance mechanisms under low but non-freezing temperatures in tropical and subtropical plants.
2023-07-14 | GSE167881 | GEO
Project description:Leaf proteomics of two different cold tolerance winter rapeseed cultivars under cold stress
2021-04-24 | PXD023323 |
Project description:Cell water permeability and cell wall properties are critical to survival of plant cells during freezing, however the underlying molecular mechanisms remain elusive. Here, we report that a specifically cold-induced nuclear protein, Tolerant to Chilling and Freezing 1 (TCF1), interacts with histones H3 and H4, and associates with chromatin containing a target gene, BLUE-COPPER-BINDING PROTEIN (BCB), encoding a glycosylphosphatidylinositol-anchored protein that regulates lignin biosynthesis. Loss of TCF1 function leads to reduced BCB transcription through affecting H3K4me2 and H3K27me3 levels within the BCB gene, resulting in reduced lignin content and enhanced freezing tolerance. Furthermore, plants with knocked-down BCB expression (amiRNA-BCB) under cold acclimation had reduced lignin accumulation, and increased freezing tolerance. The pal1pal2 double mutant (lignin content reduced by 30% compared with WT) also showed the freezing tolerant phenotype, and TCF1 and BCB act upstream of PALs to regulate lignin content. In addition, TCF1 acts independently of the CBF (C-repeat binding factor) pathway. Our findings delineate a novel molecular pathway linking the TCF1-mediated cold-specific transcriptional program to lignin biosynthesis, thus achieving cell wall remodeling with increased water permeability and consequent freezing tolerance.
2015-07-10 | GSE70682 | GEO
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.
2018-10-23 | PXD007796 | Pride
Project description:Cold stress resulting from chilling and freezing temperatures substantially inhibits plant growth and reduces crop production worldwide. Tremendous research efforts have been focused on elucidating the molecular mechanisms of freezing tolerance in plants. Little is known about the molecular nature of chilling stress responses in plants. Here we found that two allelic mutants in a spliceosome component gene SmEb (smeb-1 and smeb-2) are defective in development and responses to chilling stress. RNA-seq analysis revealed that SmEb controls the splicing of many pre-mRNAs under chilling stress. The intron retentive COP1b splicing variant was dramatically induced by chilling stress in the smeb mutants. This nuclear-depleted COP1b lacks the nuclear speckle-localization capacity, supporting the regulatory role of COP1-HY5 interaction in hypocotyl elongation during chilling stress. Genetic evidence indicates that chilling-sensitive phenotype of the smeb mutants are partially rescued by the hy5 mutation. The transcription factor BES1 shows a dramatic defect in pre-mRNA splicing in the smeb mutants. Ectopic expression of the two BES1 splicing variants enhances the chilling sensitivity of the smeb-1 mutant. Biochemical and genetic analysis showed that CBFs act as negative upstream regulators of SmEb by directly suppressing its transcription. Together, our results demonstrate that proper alternative splicing of pre-mRNAs controlled by the spliceosome component SmEb is critical for plant development and chilling stress responses. Cold stress resulting from chilling and freezing temperatures substantially inhibits plant growth and reduces crop production worldwide. Tremendous research efforts have been focused on elucidating the molecular mechanisms of freezing tolerance in plants. Little is known about the molecular nature of chilling stress responses in plants. Here we found that two allelic mutants in a spliceosome component gene SmEb (smeb-1 and smeb-2) are defective in development and responses to chilling stress. RNA-seq analysis revealed that SmEb controls the splicing of many pre-mRNAs under chilling stress. The intron retentive COP1b splicing variant was dramatically induced by chilling stress in the smeb mutants. This nuclear-depleted COP1b lacks the nuclear speckle-localization capacity, supporting the regulatory role of COP1-HY5 interaction in hypocotyl elongation during chilling stress. Genetic evidence indicates that chilling-sensitive phenotype of the smeb mutants are partially rescued by the hy5 mutation. The transcription factor BES1 shows a dramatic defect in pre-mRNA splicing in the smeb mutants. Ectopic expression of the two BES1 splicing variants enhances the chilling sensitivity of the smeb-1 mutant. Biochemical and genetic analysis showed that CBFs act as negative upstream regulators of SmEb by directly suppressing its transcription. Together, our results demonstrate that proper alternative splicing of pre-mRNAs controlled by the spliceosome component SmEb is critical for plant development and chilling stress responses.
2022-04-22 | GSE200895 | GEO
Project description:The effect of light during the development of freezing tolerance was studied in winter wheat (Triticum aestivum L. var. Mv Emese) and spring wheat variety Nadro. Ten-day-old plants were cold hardened at 5°C for 12 days either under normal (250 mmol m-2 s-1) or low light (20 mmol m-2 s-1) conditions.
2012-01-31 | GSE29640 | GEO