Whole Genome Sequencing Reveals the Effects of Recent Artificial Selection on Litter Size of Bamei Mutton Sheep
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animals and DNA Preparation
2.2. Genome Sequencing
2.3. Read Processing and Variant Calling
2.4. Population Genetics Analysis
2.5. Selective Sweep Analysis
2.6. Sanger Sequencing Validation
3. Results
3.1. Sequencing and Mapping of the Sheep
3.2. Identification of the Variation of the Sheep
3.3. Population Structure Analysis
3.4. Analysis of the Selected Loci and Candidate Genes
3.5. Mutations in the KDM4B Gene
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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Annotation Cluster 1 | Enrichment Score: 1.95 | |||
Category | Term | Count | Genes | p-Value |
KEGG_PATHWAY | oas04660:T cell receptor signaling pathway | 8 | CD3D CD3E CD3G JUN MALT1 CARD11 MAP3K14 PAK6 | 1.35 × 10−5 |
KEGG_PATHWAY | oas05142:Chagas disease (American trypanosomiasis) | 5 | CD3D CD3E CD3G JUN PLCB2 | 0.013 |
KEGG_PATHWAY | oas05166:HTLV-I infection | 6 | ATM CD3D CD3E CD3G JUN MAP3K14 | 0.072 |
KEGG_PATHWAY | oas05162:Measles | 4 | CD3D CD3E CD3G ADAR | 0.094 |
KEGG_PATHWAY | oas04640:Hematopoietic cell lineage | 3 | CD3D CD3E CD3G | 0.157 |
Annotation Cluster 2 | Enrichment Score: 0.67 | |||
Category | Term | Count | Genes | p-Value |
KEGG_PATHWAY | oas04912:GnRH signaling pathway | 3 | JUN ITPR3 PLCB2 | 0.151 |
KEGG_PATHWAY | oas04915:Estrogen signaling pathway | 3 | JUN ITPR3 PLCB2 | 0.188 |
KEGG_PATHWAY | oas04921:Oxytocin signaling pathway | 3 | JUN ITPR3 PLCB2 | 0.340 |
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Yao, Y.; Pan, Z.; Di, R.; Liu, Q.; Hu, W.; Guo, X.; He, X.; Gan, S.; Wang, X.; Chu, M. Whole Genome Sequencing Reveals the Effects of Recent Artificial Selection on Litter Size of Bamei Mutton Sheep. Animals 2021, 11, 157. https://doi.org/10.3390/ani11010157
Yao Y, Pan Z, Di R, Liu Q, Hu W, Guo X, He X, Gan S, Wang X, Chu M. Whole Genome Sequencing Reveals the Effects of Recent Artificial Selection on Litter Size of Bamei Mutton Sheep. Animals. 2021; 11(1):157. https://doi.org/10.3390/ani11010157
Chicago/Turabian StyleYao, Yaxin, Zhangyuan Pan, Ran Di, Qiuyue Liu, Wenping Hu, Xiaofei Guo, Xiaoyun He, Shangquan Gan, Xiangyu Wang, and Mingxing Chu. 2021. "Whole Genome Sequencing Reveals the Effects of Recent Artificial Selection on Litter Size of Bamei Mutton Sheep" Animals 11, no. 1: 157. https://doi.org/10.3390/ani11010157
APA StyleYao, Y., Pan, Z., Di, R., Liu, Q., Hu, W., Guo, X., He, X., Gan, S., Wang, X., & Chu, M. (2021). Whole Genome Sequencing Reveals the Effects of Recent Artificial Selection on Litter Size of Bamei Mutton Sheep. Animals, 11(1), 157. https://doi.org/10.3390/ani11010157