Expression data from roots of rice seedlings
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Oryza sativa Japonica Group
PROVIDER: GSE37161 | GEO | 2012/10/31
SECONDARY ACCESSION(S): PRJNA158587
REPOSITORIES: GEO
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2012-10-31 | E-GEOD-37161 | biostudies-arrayexpress
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Project description:Drought, salinity and sub-optimal temperatures are stresses that cause adverse effects on the growth of plants and the productivity of crops. In this study, we have analyzed the expression profiles of rice genes under control and abiotic stress conditions using microarray technology to identify the genes differentially expressed during various abiotic stresses. Experiment Overall Design: Seven-day-old light-grown rice seedlings grown under controlled conditions and those subjected to various abiotic stress conditions were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. For salt treatment (SS), the rice seedlings were transferred to a beaker containing 200 mM NaCl solution for 3 h. For desiccation (DS), rice seedlings were dried for 3 h between folds of tissue paper at 28±1 degree C, in a culture room. For cold treatment (CS), the seedlings were kept at 4±1 degree C for 3 h. The seedlings kept in water for 3 h, at 28±1 degree C, served as control (Seedling).
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Project description:Drought and salinity are two main abiotic-stresses negatively affecting crop growth and productivity worldwide with largely decreasing crop yields. The understanding of plant responses to stresses in physiology, genetics, and molecular biology will be greatly helpful to improve the tolerance of crops to abiotic-stresses through genetic engineering. To identify the genetic loci that control drought and salt tolerance in rice, we performed a large-scale screen for the mutants with altered drought and salt tolerance. A drought and salt tolerance (dst) mutant line was isolated. In this series, we compare the transcriptome of wild-type plant Zhonghua11 and dst mutants under the normal growth conditions. Keywords: genetic modification 6 samples (3 biological replicates for each line) were used in this experiment.
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Project description:According to the well-documented scenario with regard to the cytokinin-mediated phosphorelay signal transduction in Arabidopsis thaliana, certain members of the type-B ARR family are crucially implicated in the regulatory networks that are primarily propagated by the cytokinin-receptors (AHKs) in response to cytokinin. Nevertheless, clarification of the biological impact of these type-B ARR transcription factors is at a very early stage. Here we focused on a pair of highly homologous ARR10 and ARR12 genes by constructing an arr10 and arr12 double-null mutant. The mutant alleles used in this study were arr10-5 and arr12-1. arr10-5 is the SALK_098604 T-DNA insertion line, whose mutation was determined to be located in the fifth exon of the ARR10 coding sequence. arr12-1 is the SALK_054752 T-DNA insertion line, whose mutation was determined to be located in the third exon of the ARR12 coding sequence. The resulting mutant showed remarkable phenotypes with special reference to the cytokinin-action in roots (e.g., inhibition of root elongation, green callus formation from explants). Furthermore, we demonstrated that ARR10 and ARR12 are involved in the AHK-dependent signaling pathway that modulates the differentiation of root-vascular tissues (i.e., protoxylem-specification), suggesting that ARR10 and ARR12 are the prominent players that act redundantly in the AHK-dependent cytokinin signaling in roots. Keeping this in mind, we then collected the root-specific and combinatorial DNA microarray datasets with regard to the cytokinin-responsible genes by employing both the wild-type and arr10 arr12 double-mutant plants. In this study, wild-type and the arr10 arr12 mutant grown vertically on MS agar plates for 2 weeks were treated with 20 microM of the cytokinin trans-zeatin (TZ) or 0.02% DMSO (solvent for trans-zeatin solution) for 1h. These treated plant samples were divided into three portions, from which RNA samples were prepared separately from roots of seedlings with use of RNeasy Plant Mini Kit (Qiagen, Valencia, CA, U.S.A.). The quality of RNAs prepared was analyzed by Bioanalyzer 2100 (Agilent Technologies). These RNA samples were processed as recommended by the Affymetrix instruction (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetrix). These datasets will provide us with bases for understanding the early response to cytokinin on roots of seedlings in Arabidopsis thaliana.
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