Genetic Structure, Selective Signatures, and Single Nucleotide Polymorphism Fingerprints of Blue Tilapia (Oreochromis aureus), Nile Tilapia Oreochromis niloticus), and Red Tilapia (Oreochromis spp.), as Determined by Whole-Genome Resequencing
Abstract
1. Introduction
2. Results
2.1. Whole-Genome Resequencing Data Statistics
2.2. Whole-Genome SNP Statistics and Genetic Diversity Analysis
2.3. Population Genetic Structure Analysis
2.4. Population Kinship, Gene Flow, and Linkage Disequilibrium Analysis
2.5. Identification of Selected Regions in Genomes of the Three Populations and Candidate Gene Analysis
2.6. SNP Fingerprint Construction and Validation
2.7. Combinations of SNP Markers for Population Identification
3. Discussion
3.1. Genetic Diversity and Genetic Structure
3.2. Genes Selected in the Three Populations and Their Pathways and Mechanisms
3.3. SNP Fingerprint Construction
4. Materials and Methods
4.1. Sample Collection
4.2. DNA Extraction, Library Construction, and High-Throughput Sequencing
4.3. Whole Genome SNP Screening
4.4. Population Genetic Diversity Analysis
4.5. Population Genetic Structure and Population Kinship Analysis
4.6. Gene Flow and Linkage Disequilibrium Analyses
4.7. Identification of Selected Genomic Regions and Gene Enrichment Analysis
4.8. Core SNP Loci Screening and Fingerprint Construction
4.9. SNP Fingerprint Validation and Determination of SNP Marker Combinations for Population Identification
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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Hua, J.; Tao, Y.; Lu, S.; Wang, Q.; Sun, H.; Dong, Y.; Qiang, J. Genetic Structure, Selective Signatures, and Single Nucleotide Polymorphism Fingerprints of Blue Tilapia (Oreochromis aureus), Nile Tilapia Oreochromis niloticus), and Red Tilapia (Oreochromis spp.), as Determined by Whole-Genome Resequencing. Int. J. Mol. Sci. 2025, 26, 4910. https://doi.org/10.3390/ijms26104910
Hua J, Tao Y, Lu S, Wang Q, Sun H, Dong Y, Qiang J. Genetic Structure, Selective Signatures, and Single Nucleotide Polymorphism Fingerprints of Blue Tilapia (Oreochromis aureus), Nile Tilapia Oreochromis niloticus), and Red Tilapia (Oreochromis spp.), as Determined by Whole-Genome Resequencing. International Journal of Molecular Sciences. 2025; 26(10):4910. https://doi.org/10.3390/ijms26104910
Chicago/Turabian StyleHua, Jixiang, Yifan Tao, Siqi Lu, Qingchun Wang, Hui Sun, Yalun Dong, and Jun Qiang. 2025. "Genetic Structure, Selective Signatures, and Single Nucleotide Polymorphism Fingerprints of Blue Tilapia (Oreochromis aureus), Nile Tilapia Oreochromis niloticus), and Red Tilapia (Oreochromis spp.), as Determined by Whole-Genome Resequencing" International Journal of Molecular Sciences 26, no. 10: 4910. https://doi.org/10.3390/ijms26104910
APA StyleHua, J., Tao, Y., Lu, S., Wang, Q., Sun, H., Dong, Y., & Qiang, J. (2025). Genetic Structure, Selective Signatures, and Single Nucleotide Polymorphism Fingerprints of Blue Tilapia (Oreochromis aureus), Nile Tilapia Oreochromis niloticus), and Red Tilapia (Oreochromis spp.), as Determined by Whole-Genome Resequencing. International Journal of Molecular Sciences, 26(10), 4910. https://doi.org/10.3390/ijms26104910