Gene Expression
Nebulas
Gene Expression NebulasSummary: The discovery of photoperiod-sensitive male genic sterile (PGMS) lines started the development of two-line hybrid rice, which is critical to sustain production of high-yielding hybrid rice varieties. Previous reports about the PGMS lines are mainly focused on the gene cloning and their function description. The mechanisms by which PGMS lines perceive changes in photoperiod and transmit those signals to elicit downstream effects is rarely mentioned. In this work, we described the effects of photoperiod on gene expression in wild type (WT) and csa, a PGMS line, flag leaves and anthers to identify putative central factors that transduce photoperiod signals via CSA in both leaves and anthers. We also dissect the potential mechanisms that: cause csa-induced sterility under SD conditions; partially restore fertility in csa anthers under LD conditions; and finally, are responsible to restore full WT fertility under LD and SD conditions. These results provide an overview how the PGMS rice perceives and transmits photoperiod changes, and how the CSA and its homologs response to the environmental cues by regulating down-stream gene expression. That will be helpful to understand the photoperiod-sensitive mechanism and identify new photoperiod-sensitive genes.
Overall Design: At Stage12 of the anther development, flag leaves were collected at 08:00,12:00,16:00,20:00,00:00, 04:00 for a whole period under short-day(12 hours light) and long-day(14.5 hours light) condition. Anther was collected at 16:00 and 4:00 from the same tillers with the flag leaves. Each sample have two biological replicates.
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| Growth Protocol: | Oryza sativa L. ssp. japonica 9522 curtiva was grown in paddy fields of Shanghai (China) from June–August). |
| Treatment Protocol: | By the middle of August (initiation of reproductive development), the daylength is ~14.5 h (LD photoperiod). Rice plots (WT and csa) were divided into two groups, and SD photoperiod (12 h light) was simulated by covering plants in one group with lightproof plastic film from 18:00 to 6:00 of next day. |
| Extract Protocol: | Total RNA, excluding miRNAs, was extracted using TRIzol (Life Technologies) for RNA sequencing according to the manufacturer’s protocol. C |
| Library Construction Protocol: | DNA libraries were prepared with the FastQuant RT Kit with DNase (Tiangen), according to manufacturer’s instructions. |
| Molecule Type: | rRNA- RNA |
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| Library Layout: | SINGLE |
| Library Strand: | Reverse |
| Platform: | ION_TORRENT |
| Instrument Model: | Ion Torrent Proton |
| Strand-Specific: | Specific |
| 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 | Condition 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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