Effective Quality Breeding Directions—Comparison and Conservative Analysis of Hepatic Super-Enhancers between Chinese and Western Pig Breeds
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Available Public Data
2.2. ChIP-Seq Data Processing
2.3. Identification of cis-Regulatory Elements
2.4. Differential Analysis of Promoters and TEs
2.5. Identification of Conserved and Specific SEs
2.6. Motif Enrichment of Specific SEs
2.7. Comparison of Orthologous SEs and TEs
2.8. Other Bioinformatic Analysis
3. Result
3.1. Profiling of Promoter, TE, and SE in Liver
3.2. Comparison of Promoter and TE Variants across Different Porcine Breeds
3.3. Conservation and Variants of SEs in Different Breeds
3.4. Tissue Specificity of SEs
3.5. Species Specificity of SEs
4. Discussion
4.1. SEs Are Tissue-Specific ‘Network Hubs’ of cis-Elements
4.2. The Promising Application of SE in Genomic Selection Breeding
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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Zhang, Y.; Zhang, J.; Wang, C.; Qin, X.; Zhang, Y.; Liu, J.; Pan, Z. Effective Quality Breeding Directions—Comparison and Conservative Analysis of Hepatic Super-Enhancers between Chinese and Western Pig Breeds. Biology 2022, 11, 1631. https://doi.org/10.3390/biology11111631
Zhang Y, Zhang J, Wang C, Qin X, Zhang Y, Liu J, Pan Z. Effective Quality Breeding Directions—Comparison and Conservative Analysis of Hepatic Super-Enhancers between Chinese and Western Pig Breeds. Biology. 2022; 11(11):1631. https://doi.org/10.3390/biology11111631
Chicago/Turabian StyleZhang, Yi, Jinbi Zhang, Caixia Wang, Xinxin Qin, Yuge Zhang, Jingge Liu, and Zengxiang Pan. 2022. "Effective Quality Breeding Directions—Comparison and Conservative Analysis of Hepatic Super-Enhancers between Chinese and Western Pig Breeds" Biology 11, no. 11: 1631. https://doi.org/10.3390/biology11111631