A Novel Insight into the Identification of Potential SNP Markers for the Genomic Characterization of Buffalo Breeds in Pakistan
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Phenotypic Data Collection
2.2. Data Retrieval and Preprocessing
- River type = Pakistan (n = 18), India (n = 3), China (n = 23), Nepal (n = 5), Italy (n = 13), Iran (n = 20), Iraq (n = 9), and Bengal (n = 6);
- Swamp type = China (n = 99), Vietnam (n = 5), Philippines (n = 5), Laos (n = 2), Burma (n = 5), Indonesia (n = 10), and Thailand (n = 5).
2.3. Principal Component Analysis (PCA)
2.4. Admixture Analysis
2.5. Linkage Disequilibrium (LD) Decay Analysis
2.6. Identification of Breed-Specific Markers (BSMs) and Annotation
3. Results
3.1. Phenotypic Characterization
3.2. Breed Clustering Using Genomic Markers
3.3. Admixture and Linkage Disequilibrium (LD) Decay Analysis
3.4. Identification of Breed-Specific Markers (BSMs)
4. Discussion
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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Anas, M.; Farooq, M.; Asif, M.; Ali, W.R.; Mansoor, S. A Novel Insight into the Identification of Potential SNP Markers for the Genomic Characterization of Buffalo Breeds in Pakistan. Animals 2023, 13, 2543. https://doi.org/10.3390/ani13152543
Anas M, Farooq M, Asif M, Ali WR, Mansoor S. A Novel Insight into the Identification of Potential SNP Markers for the Genomic Characterization of Buffalo Breeds in Pakistan. Animals. 2023; 13(15):2543. https://doi.org/10.3390/ani13152543
Chicago/Turabian StyleAnas, Muhammad, Muhammad Farooq, Muhammad Asif, Waqas Rafique Ali, and Shahid Mansoor. 2023. "A Novel Insight into the Identification of Potential SNP Markers for the Genomic Characterization of Buffalo Breeds in Pakistan" Animals 13, no. 15: 2543. https://doi.org/10.3390/ani13152543