Gene Expression
Nebulas
Gene Expression NebulasSummary: Rice has developed several morphological and physiological strategies to adapt to phosphate starvation in the soil. In order to elucidate the molecular basis of response to phosphate starvation, we performed mRNA sequencing of 4 rice cultivars with variation in growth response to Pi starvation as indicated by the shoot/root dry weight ratio. Approximately 254 million sequence reads were mapped onto the IRGSP-1.0 reference rice genome sequence and an average of about 5,000 transcripts from each cultivar were found to be responsive under phosphate starvation. Comparative analysis of the RNA-Seq profiles of the 4 cultivars revealed similarities as well as distinct differences in expression of these responsive transcripts. We elucidated a set of core responsive transcripts including annotated and unannotated transcripts commonly expressed in the 4 cultivars but with different levels of expression. De novo assembly of unmapped reads to the Nipponbare genome generated a set of sequence contigs representing potential new transcripts that may be involved in tolerance to phosphate starvation. This study can be used for identification of genes and gene networks associated with environmental stress and the development of novel strategies for improving tolerance to phosphate starvation in rice and other cereal crops.
Overall Design: We constructed a total of 48 cDNA libraries corresponding to root and shoot of the 4 cultivars at 0 and 22 d of Pi starvation treatment with three biological replicates for each sample.
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| Growth Protocol: | Seeds of the japonica cultivars Nipponbare, IAC 25 and Vary Lava 701, and indica cultivar Kasalath were germinated and grown by hydroponic culture in Yoshida nutrient medium which consisted of 1.425 mM NH4NO3, 0.323 mM NaH2PO4, 0.513 mM K2SO4, 0.998 mM CaCl2, 1.643 mM MgSO4, 0.009 mM MnCl2, 0.075 mM (NH4)6Mo7O24, 0.019 mM H3BO3, 0.155 mM CuSO4, 0.036 mM FeCl3, 0.070 mM citric acid, and 0.152 mM ZnSO4 (Yoshida et al. 1976). |
| Treatment Protocol: | Two-week old seedlings were subjected to Pi starvation treatment by transferring in the same nutrient medium but with the Pi concentration reduced to 0.00323 mM NaH2PO4. The total dry weight of root and shoot samples from seedlings grown in Pi deficient medium and from untreated control were measured at regular intervals. Additionally, the dry weights under an overabundant supply of Pi were also determined for comparative purposes using root and shoot samples from seedlings grown in nutrient medium containing 3.23 mM NaH2PO4. The total P content per plant and P concentration in 1 mg plant sample from Pi deficient medium and control were measured as described previously (Oono et al. 2011). The inorganic Pi content was determined by releasing the cellular content of cells in water through repeated freeze–thaw cycle, and quantification with the molybdate assay method (Ames 1966). |
| Extract Protocol: | Total RNA from root and shoot samples was extracted using the TruSeq™ RNA sample preparation kit. |
| Library Construction Protocol: | Total RNA from root and shoot samples was processed for construction of cDNA libraries using the TruSeq™ RNA sample preparation kit. |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | SINGLE |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina Genome Analyzer IIx |
| Strand-Specific: | Unspecific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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