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Title: Comparative transcriptome profiling of chilling stress responsiveness in two contrasting rice genotypes      
dateReleased:
12-21-2012
description:
Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in LTH, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in LTH and strong repression in IR29. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance. In present study, comprehensive gene expression using an Affymetrix rice genome array revealed a diverse global transcription reprogramming between two rice genotypes under chilling stress and subsequent recovery conditions. The dominant change in gene expression at low temperature was up-regulation in the chilling-tolerant genotype and down-regulation in the chilling-sensitive genotype. Early responses to chilling stress common to both genotypes featured up-regulated genes related to transcription regulation and signal transduction, while functional categories of LR-chilling regulated genes were clearly diverse with a wide range of functional adaptations. At the end of the chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovery capacity at the transcriptional level. Finally, analysis of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, are involved in chilling stress tolerance. In this study, parallel transcriptomic analysis in two rice genotypes with contrasting chilling-tolerant phenotypes was performed to identify and characterize novel genes involved in chilling stress tolerance in rice.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-38023
refinement:
raw
alternateIdentifiers:
38023
keywords:
functional genomics
dateModified:
12-03-2015
availability:
available
types:
gene expression
name:
Oryza sativa
ID:
A-AFFY-126
name:
Affymetrix GeneChip Rice Genome Array [Rice]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-38023/E-GEOD-38023.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-38023/E-GEOD-38023.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38023
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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