Gene Expression
Nebulas
Gene Expression NebulasSummary: Pod dehiscence is an important agronomic trait. Pod dehiscence would cause huge yield losses before soybean maturity. Although some of soybean pod dehiscence associated genes have been identified, the underlying mechanism of pod dehiscence is still not comprehensively explained. In this study, we have identified differentially expressed genes (DEGs) between shattering-resistant and shattering-susceptible soybean accessions based on transcriptome analyses of 10 soybean accessions. Long non-coding RNAs (lncRNAs) that may be involved in soybean pod dehiscence were also identified, and we constructed co-expression networks between mRNAs and lncRNAs. RNA sequencing results were further verified by real-time PCR. Furthermore, DEGs were screened through analyzing positions of soybean pod dehiscence quantitative trait locus (QTLs) and phenotypes of soybean pod dehiscence for achieving pod-dehiscence candidate genes.
Overall Design: High-depth paired-end RNA-seq from pods of soybeans
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| Growth Protocol: | For growing soybean plants, seeds were grown on fields. |
| Treatment Protocol: | The pod dehiscence percentage was analyzed according to the previous study (Romkaew and Umezaki 2015). In brief, 50 brown pods (fully mature) were collected and kept in an oven at 60 °C for 7 h, then the number of shattering pods was counted. Pod shatteringmechanicalforce wasmeasuredusing a digital mechanical force gauge (HANDPI, China) according to the previous study (Dong et al. 2014), and at least five pods were selected and measured for each soybean accession. |
| Extract Protocol: | Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination. |
| Library Construction Protocol: | Libraries were constructed through applying TruSeq RNA (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instruction. |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500 |
| 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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