Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of rice seedlings after stress treatment

ABSTRACT: 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 28Â±1 degree C, in a culture room. For cold treatment (CS), the seedlings were kept at 4Â±1 degree C for 3 h. The seedlings kept in water for 3 h, at 28Â±1 degree C, served as control (Seedling).

ORGANISM(S): Oryza sativa

SUBMITTER: Akhilesh Tyagi

PROVIDER: E-GEOD-6901 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress.

Jain Mukesh M Nijhawan Aashima A Arora Rita R Agarwal Pinky P Ray Swatismita S Sharma Pooja P Kapoor Sanjay S Tyagi Akhilesh K AK Khurana Jitendra P JP

Plant physiology 20070209 4

F-box proteins constitute a large family in eukaryotes and are characterized by a conserved F-box motif (approximately 40 amino acids). As components of the Skp1p-cullin-F-box complex, F-box proteins are critical for the controlled degradation of cellular proteins. We have identified 687 potential F-box proteins in rice (Oryza sativa), the model monocotyledonous plant, by a reiterative database search. Computational analysis revealed the presence of several other functional domains, including le ...[more]

PMID: 17293439

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Project description:Plants initially undergo a period of vegetative development, in which it produces leaves from shoot apical meristem (SAM) and roots from the root apical meristem. Later in development, the SAM undergoes a change in fate and enters reproductive development called as floral transition, producing flowers and seeds. Our understanding of the molecular and genetic mechanisms that underlie reproductive development in plants has increased tremendously in the past decade, essentially through the work on Arabidopsis. In this study, we have analyzed the spatial and temporal gene expression in various tissues/organs and developmental stages of rice using microarray technology to identify the genes differentially expressed during various stages of reproductive development. Experiment Overall Design: Various rice tissues/organs (seedling root, mature leaf and Y leaf) and stages of reproductive (panicle and seed) development were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. We sought to obtain developmental and temporal gene expression profiles at each stage to identify the differentially expressed genes. Different stages of panicle and seed development have been categorized according to panicle length and days after pollination, respectively, based on landmark developmental events as follows: up to 0.5 mm, shoot apical meristem and rachis meristem (SAM); 0-3 cm, floral transition and floral organ development (P1); 3-10 cm, meiotic stage (P2 and P3); 10-15 cm, young microspore stage (P4); 15-22 cm, vacuolated pollen stage (P5); 22-30 cm, mature pollen stage (P6); 0-2 dap, early globular embryo (S1); 3-4 dap, middle and late globular embryo (S2); 5-10 dap, embryo morphogenesis (S3); 11-20 dap, embryo maturation (S4); 21-29, dormancy and desiccation tolerance (S5). These stage specifications are approximations based on information from Itoh et al., 2005, Plant Cell Physiol, 46, 23-47.

Dataset Information

Transcription profiling of rice seedlings after stress treatment

Publications

F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress.

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