Co-Expression Network Analysis of the Transcriptome Identified Hub Genes and Pathways Responding to Saline–Alkaline Stress in Sorghum bicolor L.
Abstract
:1. Introduction
2. Results
2.1. Phenotype of Sorghum under NaHCO3 Stress
2.2. Antioxidant System Responds to Saline–Alkali Stress
2.3. Statistics of DEGs from RNA-Seq Data
2.4. Biological Function Analysis of DEGs Corresponding to Saline–Alkaline Stress
2.5. Construction of WGCNA and Biological Function Analysis
2.6. PPI Network Validated the Key Hub Genes
2.7. Identification of DEGs Encoding Transcription Factors
2.8. Analysis of DEGs Involved in Phytohormone Biosynthesis and Signal Transduction
2.9. Analysis of DEGs Involved in Intracellular Ion Transport
2.10. Validation of RNA-Seq Via RT-qPCR
3. Discussion
4. Materials and Methods
4.1. Plant Culture and Treatments
4.2. Determination of Antioxidant Enzyme Activities, Proline and Malondialdehyde Concentrations
4.3. RNA Extraction and Transcriptome Sequencing
4.4. Transcriptome Data Quality Control and Assembly
4.5. Analysis of Functional Enrichment of DEGs
4.6. Weighted Gene Co-Expression Network Analysis (WGCNA)
4.7. Construction of the Protein–Protein Interaction (PPI) Network
4.8. Identification of Transcription Factors
4.9. Validation using Real-Time Quantitative PCR (RT-qPCR)
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
CDPK | Calcium-dependent protein kinase |
CBL | Calcineurin B-like protein |
CIPK | CBL-interacting protein kinase |
KT | Potassium transporter |
NHX | Na+/H+ antiporter |
AMT | Ammonium transporter |
NRT | Nitrate transporter |
WGCNA | Weighted gene co-expression network analysis |
PPI | Protein–protein interaction |
GO | Gene ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
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Gene Family | Gene Name | Average log2 (Fold Change) | TF Id |
---|---|---|---|
AP2/ERF-ERF | SORBI_3002G069400 | 5.628355581 | Sobic.002G069400.1.p |
SORBI_3005G103000 | 5.185617358 | Sobic.005G103000.1.p | |
SORBI_3007G205100 | 4.154163003 | Sobic.007G205100.1.p | |
SORBI_3002G269600 | 3.383162754 | Sobic.002G269600.1.p | |
SORBI_3007G162700 | 3.217188466 | Sobic.007G162700.1.p | |
BHLH | SORBI_3009G057000 | 6.300233713 | Sobic.009G057000.3.p |
SORBI_3003G077100 | 6.164343331 | Sobic.003G077100.1.p | |
SORBI_3008G153801 | 6.129472986 | Sobic.008G153801.1.p | |
SORBI_3002G267000 | 5.565088837 | Sobic.002G267000.1.p | |
SORBI_3007G008500 | 5.507180988 | Sobic.007G008500.3.p | |
MYB | SORBI_3001G056000 | 4.934458789 | Sobic.001G056000.1.p |
SORBI_3001G158600 | 3.955308363 | Sobic.001G158600.2.p | |
SORBI_3007G177100 | 2.598003641 | Sobic.007G177100.1.p | |
SORBI_3003G034500 | 2.531600604 | Sobic.003G034500.1.p | |
SORBI_3005G155900 | 2.451087788 | Sobic.005G155900.1.p | |
NAC | SORBI_3006G141900 | 7.874140412 | Sobic.006G141900.1.p |
SORBI_3001G018350 | 5.66101195 | Sobic.001G018350.1.p | |
SORBI_3003G333300 | 5.361257257 | Sobic.003G333300.1.p | |
SORBI_3005G028500 | 4.949789354 | Sobic.005G028500.1.p | |
SORBI_3002G200300 | 4.380423241 | Sobic.002G200300.1.p | |
WRKY | SORBI_3005G014200 | 7.17739049 | Sobic.005G014200.1.p |
SORBI_3010G148800 | 5.826129024 | Sobic.010G148800.1.p | |
SORBI_3008G029200 | 4.578702823 | Sobic.008G029200.1.p | |
SORBI_3009G247700 | 2.276355842 | Sobic.009G247700.1.p | |
SORBI_3007G217700 | 2.037259465 | Sobic.007G217700.6.p | |
C2H2 | SORBI_3003G242300 | 7.142275339 | Sobic.003G242300.2.p |
SORBI_3005G025100 | 6.269975035 | Sobic.005G025100.1.p | |
SORBI_3003G242400 | 5.907308008 | Sobic.003G242400.2.p | |
SORBI_3004G066700 | 3.077041905 | Sobic.004G066700.1.p | |
SORBI_3005G225700 | 2.760863094 | Sobic.005G225700.1.p |
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Wang, H.; Ye, L.; Zhou, L.; Yu, J.; Pang, B.; Zuo, D.; Gu, L.; Zhu, B.; Du, X.; Wang, H. Co-Expression Network Analysis of the Transcriptome Identified Hub Genes and Pathways Responding to Saline–Alkaline Stress in Sorghum bicolor L. Int. J. Mol. Sci. 2023, 24, 16831. https://doi.org/10.3390/ijms242316831
Wang H, Ye L, Zhou L, Yu J, Pang B, Zuo D, Gu L, Zhu B, Du X, Wang H. Co-Expression Network Analysis of the Transcriptome Identified Hub Genes and Pathways Responding to Saline–Alkaline Stress in Sorghum bicolor L. International Journal of Molecular Sciences. 2023; 24(23):16831. https://doi.org/10.3390/ijms242316831
Chicago/Turabian StyleWang, Hongcheng, Lvlan Ye, Lizhou Zhou, Junxing Yu, Biao Pang, Dan Zuo, Lei Gu, Bin Zhu, Xuye Du, and Huinan Wang. 2023. "Co-Expression Network Analysis of the Transcriptome Identified Hub Genes and Pathways Responding to Saline–Alkaline Stress in Sorghum bicolor L." International Journal of Molecular Sciences 24, no. 23: 16831. https://doi.org/10.3390/ijms242316831