Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Samples, DNA Extraction, and Whole-Genome Sequencing Data
2.2. Alignment of Short-Reads and Variant Calling
2.3. Phylogenetic, Principal Component, and Population Structure Analysis
2.4. Genetic Diversity and Genome-Wide Detection of ROHs
2.5. Estimation of Genomic Inbreeding Coefficients
2.6. Genome-Wide Identification of Selection Signals
3. Results
3.1. Abundant Genomic Variants in LSS
3.2. LSS Was Genetically Close to LST and RMN Sheep
3.3. Population Genomic Parameters and the Genome-Wide Pattern of ROH in LSS
3.4. LSS Showed Low or Moderate Inbreeding Coefficients
3.5. Selective Signatures Associated with Wool Traits in LSS
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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ROH Class | n ROH | Mean Length (kb) | Median Length (kb) | Standard Deviation | Genome Coverage (%) |
---|---|---|---|---|---|
0.1–0.2 Mb | 41274 | 137.57 | 132.02 | 27.60 | 6.56 |
0.2–0.5 Mb | 19544 | 293.39 | 273.17 | 76.36 | 6.62 |
0.5–1 Mb | 2587 | 638.84 | 604.20 | 120.10 | 1.91 |
>1 Mb | 183 | 1195.06 | 1134.59 | 200.11 | 0.25 |
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Sun, X.; Guo, J.; Li, R.; Zhang, H.; Zhang, Y.; Liu, G.E.; Emu, Q.; Zhang, H. Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep. Animals 2024, 14, 444. https://doi.org/10.3390/ani14030444
Sun X, Guo J, Li R, Zhang H, Zhang Y, Liu GE, Emu Q, Zhang H. Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep. Animals. 2024; 14(3):444. https://doi.org/10.3390/ani14030444
Chicago/Turabian StyleSun, Xueliang, Jiazhong Guo, Ran Li, Huanhuan Zhang, Yifei Zhang, George E. Liu, Quzhe Emu, and Hongping Zhang. 2024. "Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep" Animals 14, no. 3: 444. https://doi.org/10.3390/ani14030444
APA StyleSun, X., Guo, J., Li, R., Zhang, H., Zhang, Y., Liu, G. E., Emu, Q., & Zhang, H. (2024). Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep. Animals, 14(3), 444. https://doi.org/10.3390/ani14030444