DNA Methylation and Subgenome Dominance Reveal the Role of Lipid Metabolism in Jinhu Grouper Heterosis
Abstract
:1. Introduction
2. Results
2.1. Identification of DEGs
2.2. DEGs Were Affiliated to Many Amino Acid and Lipid Metabolism-Related Pathways
2.3. Metabolic Pathways Was Significantly Enriched by Trend Analysis
2.4. Candidate Modules Correlated to Growth Heterosis Were Identified by WGCNA
2.5. Identification of DMGs and KEGG Enrichment Analysis
2.6. Correlation between Gene Expression and DNA Methylation
2.7. Paternal Subgenome Dominance Was Identified by ASE Analysis
2.8. Lipid Metabolism Was Associated with EFT Heterosis
2.9. Validation of RNA-Seq Data by a qRT-PCR Assay
3. Discussion
3.1. Transcriptome and Methylome Patterns in the Hybrid and Purebred Groups
3.2. The Relationship between Transcriptome and Methylome of EFT
3.3. Paternal Subgenome Dominance Might Cause Paternal-Biased Heterosis in EFT
3.4. Lipid Metabolism Associated with EFT Heterosis Formation
3.5. “Fatty Acid Synthesis” Was Significantly Enriched in EFT
3.6. Up-Regulated Synthetic Pathways Might Explain the Higher EPA Content in EFT
3.7. Triglyceride Synthesis by Dgats Was Dominant in EFT Adipocytes
3.8. Lipids as Signaling Molecules Regulate Multiple Biological Functions in Heterosis Formation
3.9. Heterosis Analysis in EFT Gonad Development, Low-Temperature Tolerance, and Hypoxia Tolerance
4. Materials and Methods
4.1. Resources and RNA Extraction
4.2. Library Construction and Sequencing
4.3. Read Processing and Analysis of Differentially Expressed Genes (DEGs)
4.4. Trend Analysis
4.5. Weighted Gene Co-Expression Network Analysis (WGCNA)
4.6. Genomic DNA Library Construction and Bisulfite Sequencing
4.7. Data Filtering and Methylation Level Analysis
4.8. The Identification of Differentially Methylated Genes (DMGs)
4.9. The Correlation of DNA Methylation and Gene Expression in Samples
4.10. SNP Calling and ASE Analysis
4.11. Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR)
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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Liu, Y.; Wang, L.; Li, Z.; Li, L.; Chen, S.; Duan, P.; Wang, X.; Qiu, Y.; Ding, X.; Su, J.; et al. DNA Methylation and Subgenome Dominance Reveal the Role of Lipid Metabolism in Jinhu Grouper Heterosis. Int. J. Mol. Sci. 2024, 25, 9740. https://doi.org/10.3390/ijms25179740
Liu Y, Wang L, Li Z, Li L, Chen S, Duan P, Wang X, Qiu Y, Ding X, Su J, et al. DNA Methylation and Subgenome Dominance Reveal the Role of Lipid Metabolism in Jinhu Grouper Heterosis. International Journal of Molecular Sciences. 2024; 25(17):9740. https://doi.org/10.3390/ijms25179740
Chicago/Turabian StyleLiu, Yang, Linna Wang, Zhentong Li, Linlin Li, Shuai Chen, Pengfei Duan, Xinyi Wang, Yishu Qiu, Xiaoyu Ding, Jinzhi Su, and et al. 2024. "DNA Methylation and Subgenome Dominance Reveal the Role of Lipid Metabolism in Jinhu Grouper Heterosis" International Journal of Molecular Sciences 25, no. 17: 9740. https://doi.org/10.3390/ijms25179740