Gene Expression
Nebulas
Gene Expression NebulasSummary: Phosphorus (P) deficiency is a major limitation for legume crop production. Although overall adaptations of plant roots to P deficiency have been extensively studied, fragmentary information is available in regards to root nodule responses to P deficiency. In this study, genome wide transcriptome analysis was conducted using RNA-seq analysis to investigate molecular mechanisms underlying soybean (Glycine max) nodule adaptation to phosphate (Pi) starvation. Phosphorus deficiency significantly decreased soybean nodule growth and nitrogenase activity. Nodule Pi concentrations declined by 49% in response to P deficiency, but this was well below the 87% and 88% decreases observed in shoots and roots, respectively. Nodule transcript profiling revealed that a total of 2,055 genes exhibited differential expression patterns between Pi sufficient and deficient conditions. A set of DEGs appeared to be involved in maintaining Pi homeostasis in soybean nodules, including 8 Pi transporters (PTs), 8 proteins containing the SYG1/PHO81/XPR1 domain (SPXs), and 16 purple acid phosphatases (PAPs). The results suggest that a complex transcriptional regulatory network participates in soybean nodule adaption to Pi starvation, most notable a Pi signaling pathway specifically involved in maintaining Pi homeostasis in nodules.
Overall Design: Soybean seedlings were inoculated with rhizobium, then transferred into nutrient solution containing 500 mM KH2PO4 (HP) or 25 mM KH2PO4 (LP). After 25 days, nodules with the size more than 3 mm were collected for mRNA library construction and sequencing. Nodules from two plants were pooled together as one replicate, and three replicates from each P treatment were used for RNA-seq analysis.
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| Growth Protocol: | The soybean (Glycine max L.) genotype YC03-3 and rhizobium strain USDA110 were selected for hydroponic experiments. Seeds were sterilized and germinated in paper rolls for 4 days. Before transplanting, roots of uniform seedlings were inoculated with rhizobia. The nutrient solution contained KNO3 311.3 μM, NH4NO3 94.3 μM, MgCl2 25 μM, MgSO4·7H2O 500 μM, K2SO4 300 μM, MnSO4·H2O 1.5 μM, ZnSO4·7H2O 1.5 μM, CuSO4·5H2O 0.5 μM, (NH4)5MoO24·4H2O 0.16 μM, Fe-EDTA (Na) 40 μM, NaB4O7·10H2O 2.5 μM, and 25 μM KH2PO4 (LP) or 500 μM KH2PO4 (HP). The pH value was adjusted to approximately 5.8, and the nutrient solution was changed weekly. |
| Treatment Protocol: | The soybean (Glycine max L.) genotype YC03-3 and rhizobium strain USDA110 were selected for hydroponic experiments. |
| Extract Protocol: | Total RNA of nodules was isolated using Trizol reagent (Invitrogen, USA) according to the manufacturer’s protocol. The quantity and purity of total RNA was checked using a Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, USA). |
| Library Construction Protocol: | RNA libraries were prepared for sequencing using standard Illumina protocols |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | HiSeq X Ten |
| 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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