An Integration of Transcriptomic Data and Modular Gene Co-Expression Network Analysis Uncovers Drought Stress-Related Hub Genes in Transgenic Rice Overexpressing OsAbp57
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Preparation and RNA Extraction
2.2. Gene Expression Profiling, Differentially Expressed Genes (DEGs), and Enrichment Analyses
2.3. Expression Analyses of Randomly Selected Expressed Genes by qRT-PCR
2.4. Construction of Gene Co-Expression Network Modules
2.5. Gene Set Enrichment and Overrepresentation Analysis of Modules
2.6. Identification and Validation of Hub Genes
2.7. KEGG Pathway Mapping Analysis
3. Results
3.1. Global Gene Expression Profiling of the Abp57-OE Line
3.2. Modular Gene Co-Expression Analyses of the OsAbp57-OE Line
3.3. Hub Genes’ Identification in OsAbp57-OE Associated with Drought Stress
3.4. Pathway Mapping Analysis of OsAbp57-OE
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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GO Term | Ontology | Description | Number of DEGs | FDR |
---|---|---|---|---|
GO:0050896 | P | Response to stimulus | 32 | 2.20 × 10−24 |
GO:0051234 | P | Establishment of localisation | 30 | 6.00 × 10−21 |
GO:0051179 | P | Localisation | 30 | 6.00 × 10−21 |
GO:0006810 | P | Transport | 29 | 4.60 × 10−20 |
GO:0009987 | P | Cellular process | 51 | 8.40 × 10−18 |
GO:0009607 | P | Response to biotic stimulus | 14 | 8.50 × 10−18 |
GO:0006811 | P | Ion transport | 17 | 3.20 × 10−16 |
GO:0008152 | P | Metabolic process | 47 | 1.70 × 10−15 |
GO:0006950 | P | Response to stress | 17 | 5.80 × 10−12 |
GO:0042592 | P | Homeostatic process | 10 | 1.00 × 10−11 |
GO:0051704 | P | Multi-organism process | 10 | 2.30 × 10−10 |
GO:0003824 | F | Catalytic activity | 50 | 6.30 × 10−14 |
GO:0022857 | F | Transmembrane transporter activity | 17 | 7.60 × 10−14 |
GO:0005488 | F | Binding | 48 | 2.60 × 10−12 |
GO:0015075 | F | Ion transmembrane transporter activity | 13 | 2.60 × 10−12 |
GO:0005215 | F | Transporter activity | 17 | 5.00 × 10−11 |
GO:0022891 | F | Substrate-specific transmembrane transporter activity | 13 | 5.00 × 10−11 |
GO:0046872 | F | Metal ion binding | 25 | 6.60 × 10−11 |
GO:0043167 | F | Ion binding | 25 | 1.20 × 10−10 |
GO:0043169 | F | Cation binding | 25 | 1.20 × 10−10 |
GO:0022892 | F | Substrate-specific transporter activity | 13 | 2.80 × 10−10 |
Probe ID | Gene ID | Gene Name | Description | Gene Ontology | Trait Ontology | Log2FC | Up or Down |
16381052 | Os01g0100700 | RPS5-1 | 40S ribosomal protein S5-1 | Defence response to fungus, response to H2O2, ABA, salt stress, water deprivation | Oxidative stress, sheath blight disease resistance, drought and salt tolerance, ABA sensitivity | 0.04197709 | Down |
16388768 | Os01g0686800 | RACK1A | WD repeat-containing protein | Shoot and root development, seed germination, circadian rhythm, detection of redox state, defence response to fungus, ET- and SA-activated signalling pathway, SA-mediated signalling pathway, photoperiodism, response to SA, ET, salt stress, H2O2, and Cd2+ | ABA content, blast disease, disease resistance, ET sensitivity, photoperiod sensitivity, salt tolerance | 0.0606787 | Down |
16391508 | Os01g0840100 | HSP70 | Heat shock protein Hsp70 | Response to Cd2+ and stress | – | 0.09918908 | Up |
16454811 | Os02g0797400 | MCM5 | MCM family protein | Cell cycle, DNA replication | – | 0.0735361 | Down |
16444532 | Os02g0805200 | PCNA | Proliferating cell nuclear antigen | Regulation of DNA replication, double-stranded break repair, response to gamma ray, DNA damage stimulus, UV, radiation, and H2O2 | UV light sensitivity | 0.0467894 | Down |
16457043 | Os03g0152900 | KINUA | Kinesin-like protein KIN-UA | Microtubule-based movement | – | 0.13444718 | Up |
16471736 | Os03g0308800 | TPR | Tetratricopeptide-like helical domain containing protein | RNA processing, regulation of translation | – | 0.1440686 | Up |
16484814 | Os04g0598200 | RPL12 | 60S ribosomal protein L12 | Translation, ribosomal large subunit assembly, defence response to bacterium, response to heat, cold, SA, JA, H2O2, and water deprivation | Heat, cold & drought tolerance, JA sensitivity, bacterial blight disease resistance, oxidative stress | 0.1768968 | Down |
16545101 | Os08g0117200 | RPS13 | 40S ribosomal protein S13 | Translation, defence response to fungus, response to water deprivation, salt stress, ABA, H2O2 | Drought & salt tolerance, oxidative stress, sheath blight disease resistance, ABA sensitivity. | 0.93240096 | Down |
16545104 | Os08g0117300 | RPS13 | 40S ribosomal protein S13 | Translation | – | 0.0503529 | Down |
16551132 | Os09g0250700 | ABC-1 | ABC-1 domain containing protein. | – | – | 0.1204065 | Up |
16414285 | Os10g0466700 | RPL17 | 60S ribosomal protein L17 | Translation | – | 0.0262824 | Down |
16417752 | Os11g0216000 | PK | Pyruvate kinase family protein | Glycolysis | – | 0.09241819 | Up |
16388283 | Os01g0655500 | Os01g0655500 | Protein kinase, core domain containing protein. | Protein phosphorylation | – | 0.27208653 | Up |
16442445 | Os02g0618200 | PRR1 | Two-component response regulator-like PRR1 (Pseudo-response regulator 1) | Phosphorelay signal transduction system, regulation of circadian rhythm | – | 0.10612373 | Up |
16477082 | Os03g0773800 | MDH | Malate dehydrogenase | Response to ROS, metabolic processes of malate and carbohydrate, cell redox homeostasis, TCA cycle | – | 0.11776116 | Up |
16503455 | Os05g0143800 | GH3.6 | GH3 auxin-responsive promoter domain containing protein | Response to IAA, light stimulus, salt stress | Salt tolerance | 0.2140365 | Down |
16501757 | Os05g0551000 | HRZ2 | Hemerythrin motif-containing RING- and Zn-finger protein2 | Response to Fe3+ starvation, JA-mediated signalling pathway | Fe3+ sensitivity | 0.24291249 | Up |
16513254 | Os06g0308000 | TIG | Trigger factor-like protein | Protein folding and transport | – | 0.09959792 | Up |
16411623 | Os10g0111700 | PTR | POT family protein, peptide transporter | Oligopeptide transport | – | 0.20793006 | Up |
16407843 | Os10g0323600 | PRF1 | Profilin A | Cytoskeleton organisation, sequestering of actin monomers | – | 0.16372392 | Up |
16420775 | Os11g0106700 | FER1 | FERRITIN 1 | Response to Fe3+, Zn2+, H2O2, ABA, bacterdium and cold; leaf and flower development; Fe3+ transport and homeostasis; photosynthesis | – | 0.1615892 | Down |
16430188 | Os12g0106000 | FER2 | FERRITIN 2 | Response to Fe3+, Zn2+, Cu2+, H2O2, cold, bacterium, ABA; leaf and flower development; Fe3+ transport and homeostasis; photosynthesis | Temperature response trait, Cu2+ sensitivity | 0.1529454 | Down |
16427113 | Os12g0242700 | KAR | Beta-ketoacyl reductase | Fatty acid elongation | – | 0.48300481 | Up |
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Abdullah-Zawawi, M.-R.; Tan, L.-W.; Ab Rahman, Z.; Ismail, I.; Zainal, Z. An Integration of Transcriptomic Data and Modular Gene Co-Expression Network Analysis Uncovers Drought Stress-Related Hub Genes in Transgenic Rice Overexpressing OsAbp57. Agronomy 2022, 12, 1959. https://doi.org/10.3390/agronomy12081959
Abdullah-Zawawi M-R, Tan L-W, Ab Rahman Z, Ismail I, Zainal Z. An Integration of Transcriptomic Data and Modular Gene Co-Expression Network Analysis Uncovers Drought Stress-Related Hub Genes in Transgenic Rice Overexpressing OsAbp57. Agronomy. 2022; 12(8):1959. https://doi.org/10.3390/agronomy12081959
Chicago/Turabian StyleAbdullah-Zawawi, Muhammad-Redha, Lay-Wen Tan, Zuraida Ab Rahman, Ismanizan Ismail, and Zamri Zainal. 2022. "An Integration of Transcriptomic Data and Modular Gene Co-Expression Network Analysis Uncovers Drought Stress-Related Hub Genes in Transgenic Rice Overexpressing OsAbp57" Agronomy 12, no. 8: 1959. https://doi.org/10.3390/agronomy12081959
APA StyleAbdullah-Zawawi, M. -R., Tan, L. -W., Ab Rahman, Z., Ismail, I., & Zainal, Z. (2022). An Integration of Transcriptomic Data and Modular Gene Co-Expression Network Analysis Uncovers Drought Stress-Related Hub Genes in Transgenic Rice Overexpressing OsAbp57. Agronomy, 12(8), 1959. https://doi.org/10.3390/agronomy12081959