Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA
Abstract
:1. Introduction
2. Results
2.1. Physiological Changes in Quinoa Seedlings under Low-Temperature Stress
2.2. Construction of Gene Co-Expression Network
2.3. GO and KEGG Enrichment Analysis of Relevant Specificity Modules
2.4. Identification of Core Genes and Construction of Interaction Network
2.5. Transcription Factors under Low-Temperature Stress
2.6. Real-Time Fluorescence Quantitative PCR Validation
3. Discussion
4. Materials and Methods
4.1. Quinoa Planting and Growing Conditions
4.2. Data Acquisition
4.3. Physiological Indicators
4.4. Construction of Weighted Gene Co-Expression Network Analysis
4.5. Identification of Specific Modules and GO and KEGG Functional Enrichment Analysis
4.6. Identification of Core Genes of Specific Modules and Construction of Gene Interaction Network
4.7. Identification of Transcription Factors
4.8. Real-Time Fluorescence Quantitative PCR Validation
4.9. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Proline | Malondialdehyde | Soluble Sugar | Peroxidase | Soluble Protein | Total Chlorophyll | |
---|---|---|---|---|---|---|
Proline | 1 | |||||
Malondialdehyde | −0.519 * | 1 | ||||
Soluble sugar | 0.414 | −0.059 | 1 | |||
Peroxidase | −0.395 | −0.022 | 0.037 | 1 | ||
Soluble protein | −0.186 | 0.168 | −0.095 | −0.397 | 1 | |
Total chlorophyll | −0.199 | −0.692 ** | −0.088 | −0.599 ** | 0.112 | 1 |
Module | Module Candidate Hub Genes | TFs Family | Gene Function |
---|---|---|---|
Turquoise | gene-LOC110684437 | AP2/ERF | Ethylene-responsive transcription factor RAP2-12-like |
gene-LOC110697250 | - | Pre-mRNA-processing factor 19-like | |
gene-LOC110709726 | - | 14-3-3 protein 10-like | |
gene-LOC110726534 | - | Eukaryotic peptide chain release factor subunit 1-3 | |
gene-LOC110722386 | - | Zinc finger CCCH domain-containing protein 40-like | |
gene-LOC110733109 | - | E3 ubiquitin-protein ligase Hakai-like | |
Gray | gene-LOC110731664 | MYB-related | Protein LHY-like |
gene-LOC110736639 | NAC | NAC domain-containing protein 2-like | |
gene-LOC110733919 | C2C2-CO-like | Zinc finger protein CONSTANS-LIKE 6-like | |
gene-LOC110683707 | - | 40S ribosomal protein S23 | |
gene-LOC110718876 | - | Uncharacterized LOC110718876 | |
gene-LOC110720903 | AP2/ERF | Ethylene-responsive transcription factor 3-like |
Quantity | Gene-ID | NCBI-Gene ID | Primer | 5′ to 3′ |
---|---|---|---|---|
1 | gene-LOC110722386 | 110722386 | Forward primer | AAGAGTGATGTCAATAGG |
Reverse primer | CCGTAAGAGGATTCATAA | |||
2 | gene-LOC110733109 | 110733109 | Forward primer | GACTCAATTTGCTATCTATG |
Reverse primer | TCACTCATCTCTTCTCTT | |||
3 | gene-LOC110733919 | 110733919 | Forward primer | AAGCAAGAGTATCAAGAT |
Reverse primer | TCAACTTCCTAACTTCATA | |||
4 | gene-LOC110683707 | 110683707 | Forward primer | CTTACAAGAAGTCACATCT |
Reverse primer | AGTTCAAACAACCATCAT | |||
5 | gene-LOC110718876 | 110718876 | Forward primer | GGATTGGATGAGAATAACT |
Reverse primer | GCTCTTAACCTCTGTAAC | |||
6 | gene-LOC110720903 | 110720903 | Forward primer | TCTAATCACCACCATCAA |
Reverse primer | CTCAACCGTACTACTCAT | |||
Internal reference gene | ACT-1 | 818339 | Forward primer | GTCCACAGAAAGTGCTTCTAAG |
Reverse primer | AACAACTCCTCACCTTCTCATG |
Component | Volume (µL) |
---|---|
2× PerfectStartTM SYBR qPCR Supermix | 10 |
Passive Reference Dye (50×) (optional) | 0.4 |
Nuclease-free Water | 6.8 |
Forward Primer (10 μM) | 0.4 |
Reverse Primer (10 μM) | 0.4 |
cDNA (200 µg/µL) | 2 |
Total volume | 20 |
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Zhang, L.; Jiang, G.; Wang, X.; Bai, Y.; Zhang, P.; Liu, J.; Li, L.; Huang, L.; Qin, P. Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA. Int. J. Mol. Sci. 2024, 25, 6885. https://doi.org/10.3390/ijms25136885
Zhang L, Jiang G, Wang X, Bai Y, Zhang P, Liu J, Li L, Huang L, Qin P. Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA. International Journal of Molecular Sciences. 2024; 25(13):6885. https://doi.org/10.3390/ijms25136885
Chicago/Turabian StyleZhang, Lingyuan, Guofei Jiang, Xuqin Wang, Yutao Bai, Ping Zhang, Junna Liu, Li Li, Liubin Huang, and Peng Qin. 2024. "Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA" International Journal of Molecular Sciences 25, no. 13: 6885. https://doi.org/10.3390/ijms25136885