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| Status |
Public on Dec 10, 2011 |
| Title |
Global Identification of Potential Gene Biomarkers Associated with Ozone-induced Foliar Injury in Rice Seedling Leaves by Correlating their Symptom Severity with Transcriptome Profiling |
| Platform organism |
Oryza sativa Japonica Group |
| Sample organism |
Oryza sativa |
| Experiment type |
Expression profiling by array
|
| Summary |
A combined approach of evaluating ozone (O3)-caused foliar injury symptom and global gene expression profiling was used to identify potential genes associated with severity of injury on leaves of O3 (200 ppb)-fumigated (1, 12, 24, 48, and 72 h) two-week-old rice (cv. Nipponbare) seedling along with appropriate control. Foliar injuries were evaluated up to 72 h using both qualitative visual scale and quantitative RGB (red-green-blue) image analysis methods. The (R-G)/(R+G) was found as the optimal quantitative RGB parameter to assess the foliar injury. Large-scale transcript profiling of leaves identified 270 genes linked with foliar injury. Of these genes, the expression levels of 139 genes showed significant differences (P < 0.05) between leaves without and with injury symptoms. When a rigorous correlation test was applied on these genes for their expression changes and relative (R-G)/(R+G) parameters, the expression of 93 genes were found to increase with increased foliar severity up to 72 h, showing a positive, tight correlation between a subset of gene expression and commonly observed O3-triggerred symptom of foliar injury with correlation coefficient below -0.80. Of 93 genes, genes involved in metabolism (29%) formed a major functional category. Reconstruction of the metabolic networks with identified metabolic genes provided insight into the cellular responses such as photorespiration, biosynthesis of secondary metabolites, and detoxification. The O3 effect on these cellular responses has been previously reported based on physiological and biochemical studies, validating our approach used in this study to globally identify O3-responsive biomarkers tightly linked with foliar injury symptom. This study provides evidence for the presence of large number of genes associated with the foliar injury symptom than thought before, and could serve as a resource of potential biomarkers to study mechanisms of visible injury development by O3.
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| Overall design |
Comparison between healthy rice seedling leaves and ozone treated (for 48 h and 72 h) rice seedling leaves was performed. Three biological replicates (5 leaves in each replicate; pooled) were used, and dye-swaped.
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| Contributor(s) |
Cho K, Kubo A, Shibato J, Agrawal GK, Saji H, Rakwal R |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Dec 08, 2011 |
| Last update date |
Dec 06, 2012 |
| Contact name |
RANDEEP RAKWAL |
| E-mail(s) |
plantproteomics@gmail.com
|
| Phone |
+81-(0)90-1853-7875
|
| Organization name |
University of Tsukuba
|
| Department |
Institute of Health and Sport Sciences
|
| Lab |
GSI 403
|
| Street address |
1-1-1 Tennodai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8574 |
| Country |
Japan |
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| Platforms (1) |
| GPL892 |
Agilent-012106 Rice Oligo Microarray G4138A (Feature Number version) |
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| Samples (4)
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| GSM845899 |
Healthy 0 h Control (Cy3)_O3 48 h (Cy5)_Pooled 1 |
| GSM845904 |
Healthy 0 h Control (Cy5)_O3 48 h (Cy3)_Pooled 2 |
| GSM845921 |
Healthy 0 h Control (Cy3)_O3 72 h (Cy5)_Pooled 1 |
| GSM845922 |
Healthy 0 h Control (Cy5)_O3 72 h (Cy3)_Pooled 2 |
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| Relations |
| BioProject |
PRJNA149757 |
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