Genome-Wide SNP Analysis for Milk Performance Traits in Indigenous Sheep: A Case Study in the Egyptian Barki Sheep
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animals and Phenotypes
2.2. Genotyping and Quality Control
2.3. Genome Wide FST Calculation
3. Results
3.1. Phenotypic Data of Milk Performance Traits
3.2. Detection of Genomic Regions and Candidate Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Trait | Group * | N | Mean | SE | Min | Max | p Value ** |
---|---|---|---|---|---|---|---|
Milk yield MY (kg) | HMY | 25 | 41.97 | 2.02 | 31.50 | 72.00 | p < 0.001 |
LMY | 25 | 17.20 | 0.71 | 9.90 | 23.40 | ||
Milk quality (MQ; PC1) | HMQ | 25 | −1.11 | 0.08 | −0.63 | −2.21 | p < 0.001 |
LMQ | 25 | 2.05 | 0.29 | 4.91 | 0.14 | ||
Milk fat (%) | HMQ | 25 | 6.28 | 0.26 | 4.78 | 9.60 | p < 0.001 |
LMQ | 25 | 2.61 | 0.13 | 1.45 | 3.60 | ||
Milk protein (%) | HMQ | 25 | 6.85 | 0.25 | 5.20 | 9.20 | p < 0.001 |
LMQ | 25 | 4.09 | 0.10 | 2.85 | 4.60 | ||
Milk lactose (%) | HMQ | 25 | 7.99 | 0.14 | 7.30 | 9.90 | p < 0.001 |
LMQ | 25 | 5.14 | 0.22 | 1.01 | 6.10 | ||
Total solids (%) | HMQ | 25 | 25.49 | 0.87 | 20.00 | 33.10 | p < 0.001 |
LMQ | 25 | 14.83 | 0.18 | 12.68 | 16.24 |
Trait | MY | Fat | Protein | Lactose | Total Solids | PC1 |
---|---|---|---|---|---|---|
MY | 1 | |||||
Fat | −0.12 | 1 | ||||
Protein | −0.05 | 0.38 ** | 1 | |||
Lactose | 0.05 | 0.26 ** | 0.29 ** | 1 | ||
Total Solids | 0.06 | 0.47 ** | 0.83 ** | 0.43 ** | 1 | |
PC1 | −0.06 | 0.69 ** | 0.90 ** | 0.61 ** | 0.94 ** | 1 |
Trait | Rs Name | Chr | Position | MAF | FST | Z(FST) | Candidate Genes * |
---|---|---|---|---|---|---|---|
Milk yield | rs412092721 | 1 | 158753375 | 0.477 | 0.263 | 10.68 | ENSOARG00000017360 |
rs428217479 | 3 | 164177406 | 0.429 | 0.278 | 11.32 | OR6C76, OR6C1, OR6C75 | |
rs430736025 | 3 | 169823214 | 0.374 | 0.270 | 10.99 | GAS2L3, SLC5A8, ANO4 | |
rs420351948 | 4 | 109338529 | 0.332 | 0.319 | 13.07 | ENSOARG00000001351 | |
rs399050266 | 4 | 113362135 | 0.350 | 0.254 | 10.30 | NUB1, RHEB | |
rs418394216 | 6 | 57451934 | 0.201 | 0.255 | 10.34 | TBC1D1, KLF3 | |
rs427343726 | 12 | 15424350 | 0.228 | 0.287 | 11.70 | ENSOARG00000025431, ENSOARG00000025432 | |
rs412626910 | 12 | 79966574 | 0.421 | 0.247 | 10.04 | CRB1, DENND1B | |
rs430297634 | 18 | 11841541 | 0.433 | 0.259 | 10.53 | MCTP2 | |
rs423654488 | 19 | 15202234 | 0.352 | 0.281 | 11.48 | GASK1A, ANO10, SNRK-ABHD5 | |
Milk quality | rs408700818 | 3 | 220103217 | 0.370 | 0.300 | 10.14 | ATXN10, FBLN1, PPARA |
rs414244120 | 3 | 220048441 | 0.485 | 0.299 | 10.09 | FBLN1, ATXN10, PPARA |
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Abousoliman, I.; Reyer, H.; Oster, M.; Murani, E.; Mohamed, I.; Wimmers, K. Genome-Wide SNP Analysis for Milk Performance Traits in Indigenous Sheep: A Case Study in the Egyptian Barki Sheep. Animals 2021, 11, 1671. https://doi.org/10.3390/ani11061671
Abousoliman I, Reyer H, Oster M, Murani E, Mohamed I, Wimmers K. Genome-Wide SNP Analysis for Milk Performance Traits in Indigenous Sheep: A Case Study in the Egyptian Barki Sheep. Animals. 2021; 11(6):1671. https://doi.org/10.3390/ani11061671
Chicago/Turabian StyleAbousoliman, Ibrahim, Henry Reyer, Michael Oster, Eduard Murani, Ismail Mohamed, and Klaus Wimmers. 2021. "Genome-Wide SNP Analysis for Milk Performance Traits in Indigenous Sheep: A Case Study in the Egyptian Barki Sheep" Animals 11, no. 6: 1671. https://doi.org/10.3390/ani11061671