Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide Mapping of the Ozone-responsive Transcriptomes of Rice Panicle and Seed Tissues Reveals Novel Insight into their Regulatory Events

ABSTRACT: The ‘O3-responsive transcriptome’ behavior in the panicles and grains of rice plant was studied individually through high-throughput oligo-DNA microarray technique. Obtained results showed that O3 differentially regulated 620 and 130 genes in the panicles and grains separately, by at least two-fold changes. However, only five genes were found to be common in both the tissues, suggesting towards the tissue specific O3-sensitivity in rice plants. Among the O3-responsive genes, 176 and 444 genes were up- and down-regulated in rice panicle; whereas, 24 and 106 genes in rice grain, respectively. Further mapping onto various regulatory events revealed that, the majority of differentially expressed genes were mainly involved in signaling, hormonal, cell wall, transcription, proteolysis, and defense events. Many previously unknown O3-responsive novel genes were identified, including the brassinosteroid insensitive-1 receptor kinase, wall-associated kinase like receptor, calcium-dependent protein kinases, phosphatidylinositol kinases, G-protein components, ethylene insensitive-3, cellulose synthases, pectatelyase, etc. Inventory of 745 O3-responsive genes and their mapping will surely expand our knowledge on novel regulatory processes in both panicles and grains of rice; and, serve as a resource towards the designing of rice crops for future high-O3 world. Comparison between healthy rice plant panicles and ozone treated plant panicles (for 8 h) and seed (grain) of healthy rice plants and of rice plants grown under ozone for their lifeftime was performed. Three biological replicates (panicle or seed; pooled) were used, and dye-swaped.

ORGANISM(S): Oryza sativa

SUBMITTER: Randeep Rakwal

PROVIDER: E-GEOD-37478 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description: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. 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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Genome-wide Mapping of the Ozone-responsive Transcriptomes of Rice Panicle and Seed Tissues Reveals Novel Insight into their Regulatory Events

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