Unravelling the Genetic Architecture of Serum Biochemical Indicators in Sheep
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animal Population and Blood Serum Indicators
2.2. Genotyping and Quality Control
2.3. Estimation of Genetic Parameters
2.4. Genome-Wide Association Studies (GWASs)
2.5. Functional Annotation Analysis
3. Results
3.1. Phenotypic Correlation between and Genetic Parameter Analyses of Serum Biochemical Indicators
3.2. Genome-Wide Association Studies (GWASs)
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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Traits | N | Minimum | Mean | SD | Maximum |
---|---|---|---|---|---|
ALT | 417 | 5 | 12.64 | 4.21 | 27 |
AST | 393 | 40 | 78.04 | 18.24 | 141 |
CHO | 415 | 21 | 45.99 | 14.35 | 85 |
LDH | 400 | 228 | 494.69 | 111.48 | 912 |
CA | 415 | 5.20 | 8.11 | 1.02 | 13.10 |
IP | 410 | 2.90 | 5.85 | 1.04 | 9.60 |
CRE | 422 | 0.33 | 0.53 | 0.08 | 0.91 |
GLU | 422 | 29 | 60.11 | 10.51 | 92 |
TPRO | 418 | 36.29 | 54.11 | 7.39 | 76.96 |
UREA | 414 | 11 | 43.01 | 9.39 | 84 |
Traits | ALT | AST | CHO | LDH | CA | IP | CRE | GLU | TPRO | UREA |
---|---|---|---|---|---|---|---|---|---|---|
ALT | 0.21 ± 0.11 | 0.48 ± 0.04 | 0.18 ± 0.04 | 0.49 ± 0.04 | −0.01 ± 0.05 | 0.22 ± 0.04 | −0.01 ± 0.05 | 0.02 ± 0.05 | 0.35 ± 0.04 | 0.09 ± 0.05 |
AST | 0.91 ± 0.08 | 0.14 ± 0.10 | 0.40 ± 0.04 | 0.53 ± 0.04 | 0.28 ± 0.04 | 0.18 ± 0.04 | 0.30 ± 0.04 | 0.14 ± 0.05 | 0.47 ± 0.04 | 0.27 ± 0.04 |
CHO | 0.48 ± 0.16 | 0.77 ± 0.12 | 0.43 ± 0.14 | 0.35 ± 0.04 | 0.19 ± 0.04 | 0.26 ± 0.04 | 0.20 ± 0.04 | 0.19 ± 0.04 | 0.54 ± 0.04 | 0.32 ± 0.04 |
LDH | 0.82 ± 0.08 | 0.87 ± 0.07 | 0.70 ± 0.13 | 0.36 ± 0.14 | 0.14 ± 0.05 | 0.32 ± 0.04 | 0.14 ± 0.04 | 0.20 ± 0.04 | 0.52 ± 0.04 | 0.07 ± 0.06 |
CA | −0.03 ± 0.20 | 0.64 ± 0.12 | 0.39 ± 0.11 | 0.36 ± 0.14 | 0.27 ± 0.13 | 0.11 ± 0.05 | 0.99 ± 0.01 | 0.24 ± 0.04 | 0.35 ± 0.04 | 0.28 ± 0.04 |
IP | 0.84 ± 0.23 | 0.88 ± 0.33 | 0.53 ± 0.14 | 0.80 ± 0.15 | 0.37 ± 0.17 | 0.29 ± 0.13 | 0.10 ± 0.05 | 0.19 ± 0.04 | 0.36 ± 0.04 | −0.10 ± 0.05 |
CRE | −0.04 ± 0.22 | 0.66 ± 0.12 | 0.42 ± 0.11 | 0.28 ± 0.14 | 0.11 ± 0.06 | 0.35 ± 0.19 | 0.20 ± 0.11 | 0.23 ± 0.04 | 0.34 ± 0.04 | 0.29 ± 0.04 |
GLU | 0.13 ± 0.23 | 0.77 ± 0.34 | 0.54 ± 0.19 | 0.78 ± 0.25 | 0.61 ± 0.14 | 0.76 ± 0.24 | 0.62 ± 0.15 | 0.15 ± 0.10 | 0.23 ± 0.04 | −0.11 ± 0.05 |
TPRO | 0.71 ± 0.12 | 0.81 ± 0.09 | 0.81 ± 0.07 | 0.98 ± 0.08 | 0.64 ± 0.09 | 0.80 ± 0.13 | 0.64 ± 0.10 | 0.59 ± 0.17 | 0.55 ± 0.14 | 0.21 ± 0.04 |
UREA | 0.27 ± 0.32 | 0.73 ± 0.17 | 0.74 ± 0.14 | 0.29 ± 0.34 | 0.76 ± 0.16 | −0.52 ± 0.38 | 0.78 ± 0.15 | −0.63 ± 0.46 | 0.59 ± 0.18 | 0.18 ± 0.11 |
Trait | SNP | Chr | Oar_v4.0 Position (bp) | p-Value | MAF | Effect Size | Candidate Gene | Distance |
---|---|---|---|---|---|---|---|---|
CHO | rs415766081 | 1 | 107,828,780 | 1.022 × 10−06 | 0.110 | 0.084 | Spectrin α, erythrocytic 1 (SPTA1) | Intron variant |
CA | rs427096440 | 17 | 17,753,256 | 8.033 × 10−07 | 0.414 | 0.004 | Microsomal glutathione S-transferase 2 (MGST2) | ~31 Kb upstream |
CRE | rs423178582 | 22 | 37,960,974 | 7.716 × 10−07 | 0.157 | 0.068 | CDK2 associated cullin domain 1 (CACUL1) | ~42 Kb upstream |
GLU | rs428784360 | 2 | 227,357,948 | 1.207 × 10−07 | 0.160 | 0.092 | ENSOARG00020040484.1 | Intron variant |
LDH | rs410665381 | 6 | 72,632,996 | 1.216 × 10−06 | 0.129 | 0.117 | Insulin-like growth factor binding protein 7 (IGFBP7) | ~267 Kb upstream |
IP | rs404995480 | 13 | 17,678,848 | 6.902 × 10−07 | 0.388 | 0.063 | Par-3 family cell polarity regulator (PARD3) | Intron variant |
Trait | SNP | Chr | Oar_v4.0 Position (bp) | p-Value | MAF | Effect Size | Candidate Gene | Distance |
---|---|---|---|---|---|---|---|---|
CHO | rs415259159 | 11 | 36,648,365 | 1.536 × 10−05 | 0.417 | 0.047 | Prohibitin 1 (PHB1) | ~35 Kb upstream |
CHO | rs408900631 | 3 | 198,343,644 | 2.820 × 10−05 | 0.432 | 0.047 | Solute Carrier Family 15 Member 5 (SLC15A5) | ~55 Kb downstream |
CHO | rs403535835 | 5 | 75,927,368 | 2.923 × 10−05 | 0.101 | 0.073 | LOC101117162 | ~19 Kb upstream |
ALT | rs413251030 | 2 | 38,421,272 | 7.175 × 10−06 | 0.194 | 0.380 | Tripartite Motif Containing 35 (TRIM35) | ~71 Kb downstream |
ALT | rs421887664 | 7 | 80,842,728 | 3.158 × 10−05 | 0.158 | 0.439 | Regulator of G-Protein Signaling 6 (RGS6) | Intron variant |
AST | rs405842437 | 14 | 24,175,813 | 1.453 × 10−05 | 0.449 | 0.013 | Nucleoporin 93 (NUP93) | Intron variant |
AST | rs423986212 | 4 | 109,758,783 | 3.111 × 10−05 | 0.269 | 0.014 | Contactin Associated Protein 2 (CNTNAP2) | Intron variant |
CA | rs421266853 | 8 | 39,031,937 | 1.967 × 10−05 | 0.417 | 0.003 | LOC105611309 | ~56 Kb downstream |
CA | rs408365736 | 17 | 19,135,137 | 2.576 × 10−05 | 0.077 | 0.006 | Solute Carrier Family 7 Member 11 (SLC7A11) | Intron variant |
GLU | rs412782784 | 1 | 257,987,356 | 7.143 × 10−06 | 0.067 | 0.118 | β-1,3-Galactosyltransferase 5 (B3GALT5) | ~288 Kb downstream |
GLU | rs410943504 | 2 | 178,724,382 | 7.415 × 10−06 | 0.457 | 0.059 | Dipeptidyl Peptidase Like 10 (DPP10) | Intron variant |
LDH | rs402703943 | 1 | 63,683,463 | 1.665 × 10−05 | 0.218 | 0.090 | Heparan Sulfate 2-O-Sulfotransferase 1 (HST2ST1) | ~185 Kb downstream |
LDH | rs410138359 | 13 | 18,806,069 | 1.678 × 10−05 | 0.169 | 0.087 | Neuropilin 1 (NRP1) | ~44 Kb downstream |
IP | rs420848991 | 2 | 168,420,121 | 4.201 × 10−06 | 0.191 | 0.077 | LDL Receptor Related Protein 1B (LRP1B) | Intron variant |
TPRO | rs423075621 | 8 | 963,780 | 2.017 × 10−05 | 0.488 | 0.045 | LOC101118029 | ~74 Kb upstream |
TPRO | rs401111582 | 7 | 79,289,788 | 2.319 × 10−05 | 0.386 | 0.044 | Mitogen-Activated Protein 3 Kinase 9 (MAP3K9) | Intron variant |
UREA | rs403791299 | 18 | 48,405,490 | 5.277 × 10−06 | 0.432 | 1.971 | LOC101103187 | ~127 Kb upstream |
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Kizilaslan, M.; Arzik, Y.; Behrem, S.; Yavuz, E.; White, S.N.; Cinar, M.U. Unravelling the Genetic Architecture of Serum Biochemical Indicators in Sheep. Genes 2024, 15, 990. https://doi.org/10.3390/genes15080990
Kizilaslan M, Arzik Y, Behrem S, Yavuz E, White SN, Cinar MU. Unravelling the Genetic Architecture of Serum Biochemical Indicators in Sheep. Genes. 2024; 15(8):990. https://doi.org/10.3390/genes15080990
Chicago/Turabian StyleKizilaslan, Mehmet, Yunus Arzik, Sedat Behrem, Esra Yavuz, Stephen N. White, and Mehmet Ulas Cinar. 2024. "Unravelling the Genetic Architecture of Serum Biochemical Indicators in Sheep" Genes 15, no. 8: 990. https://doi.org/10.3390/genes15080990