 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 21, 2012 |
| Title |
Comparative transcriptome profiling of chilling stress responsiveness in two contrasting rice genotypes |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by array
|
| Summary |
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.
|
| |
|
| Overall design |
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.
|
| |
|
| Contributor(s) |
Zhang T, Zhao X, Pan Y, Huang L, Liu X, Zong Y, Zhu L, Yang D, Fu B |
| Citation(s) |
22912843 |
| |
| Submission date |
May 17, 2012 |
| Last update date |
Dec 27, 2017 |
| Contact name |
ting zhang |
| Organization name |
Chinese Acadamy of agricultural science
|
| Street address |
zhongguancun south street 12
|
| City |
beijing |
| State/province |
beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL2025 |
[Rice] Affymetrix Rice Genome Array |
|
| Samples (36)
|
| GSM932406 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-control, biological rep1 |
| GSM932407 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-control, biological rep2 |
| GSM932408 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-control, biological rep3 |
| GSM932409 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-2h, biological rep1 |
| GSM932410 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-2h, biological rep2 |
| GSM932411 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-2h, biological rep3 |
| GSM932412 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-8h, biological rep1 |
| GSM932413 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-8h, biological rep2 |
| GSM932414 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-8h, biological rep3 |
| GSM932415 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-24h, biological rep1 |
| GSM932416 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-24h, biological rep2 |
| GSM932417 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-24h, biological rep3 |
| GSM932418 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-48h, biological rep1 |
| GSM932419 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-48h, biological rep2 |
| GSM932420 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-48h, biological rep3 |
| GSM932421 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-recovery-24h, biological rep1 |
| GSM932422 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-recovery-24h, biological rep2 |
| GSM932423 |
Rice-Li-Jiang-Xin-Tuan-Hei-Gu-recovery-24h, biological rep3 |
| GSM932424 |
Rice-IR29-control, biological rep1 |
| GSM932425 |
Rice-IR29-control, biological rep2 |
| GSM932426 |
Rice-IR29-control, biological rep3 |
| GSM932427 |
Rice-IR29-cold-2h, biological rep1 |
| GSM932428 |
Rice-IR29-cold-2h, biological rep2 |
| GSM932429 |
Rice-IR29-cold-2h, biological rep3 |
| GSM932430 |
Rice-IR29-cold-8h, biological rep1 |
| GSM932431 |
Rice-IR29-cold-8h, biological rep2 |
| GSM932432 |
Rice-IR29-cold-8h, biological rep3 |
| GSM932433 |
Rice-IR29-cold-24h, biological rep1 |
| GSM932434 |
Rice-IR29-cold-24h, biological rep2 |
| GSM932435 |
Rice-IR29-cold-24h, biological rep3 |
| GSM932436 |
Rice-IR29-cold-48h, biological rep1 |
| GSM932437 |
Rice-IR29-cold-48h, biological rep2 |
| GSM932438 |
Rice-IR29-cold-48h, biological rep3 |
| GSM932439 |
Rice-IR29-recovery-24h, biological rep1 |
| GSM932440 |
Rice-IR29-recovery-24h, biological rep2 |
| GSM932441 |
Rice-IR29-recovery-24h, biological rep3 |
|
| Relations |
| BioProject |
PRJNA167100 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE38023_RAW.tar |
142.9 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
|
|
|
|
 |
Less...
More...