GRM1 as a Candidate Gene for Buffalo Fertility: Insights from Genome-Wide Association Studies and Its Role in the FOXO Signaling Pathway
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Phenotypes and Animal Resources
2.3. Sample Collection and Sequencing
2.4. Alignments and Variant Identification
2.5. Variation Filtering
2.6. Principal Component Analysis
2.7. Population Structure Analysis
2.8. Genome-Wide Association Mapping
2.9. Pathway Enrichment and Protein–Protein Interaction
2.10. Statistical Analysis
3. Results
3.1. Phenotypic Value Statistics of the Traits
3.2. Population Structure
3.3. Results of the Genome-Wide Associations
3.4. Kyoto Encyclopedia of Genes and Genomes Pathway Analysis of Candidate Genes
3.5. Significant Association of Fertility with SNP Validation
4. Discussion
4.1. Population Stratification
4.2. Genome-Wide Association Analysis of Reproductive-Related Traits
4.3. The Mechanism of SNP Mutation and Fertility Traits
4.4. Discussion of Tradeoffs
4.5. Limitations and Future Directions
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 | Mean | SD | Min | Max |
---|---|---|---|---|
AFC | 3.67 | 0.88 | 2.17 | 6.54 |
Methods | SNP | Chr | Pos | p | R2 | Candidate Genes |
---|---|---|---|---|---|---|
SUPER/GLM(Q)/Blink/FarmCPU | 1 | NC_037554.1 | 20,660,384 | 5.0621 × 10−8 | 0.49381 | GRM1 |
SUPER/GLM(Q)/Blink/FarmCPU | 2 | NC_037556.1 | 50,669,172 | 6.5734 × 10−8 | 0.42667 | -- |
SUPER/GLM(Q) | 3 | NC_037545.1 | 35,877,289 | 6.8853 × 10−8 | 0.34081 | -- |
SUPER/GLM(Q) | 4 | NC_037546.1 | 31,601,350 | 3.7412 × 10−9 | 0.41127 | OPN5 |
SUPER/GLM(Q) | 5 | NC_037548.1 | 4,405,934 | 6.4571 × 10−8 | 0.33847 | FAM118A; UPK3A; KIAA0930 |
SUPER/GLM(Q) | 6 | NC_037548.1 | 157,620,852 | 5.3121 × 10−8 | 0.3642 | -- |
SUPER/GLM(Q) | 7 | NC_037551.1 | 20,700,724 | 8.906 × 10−9 | 0.3905 | -- |
SUPER/GLM(Q) | 8 | NC_037551.1 | 52,947,579 | 1.05 × 10−7 | 0.35825 | -- |
SUPER/GLM(Q) | 9 | NC_037552.1 | 24,460 | 6.7407 × 10−8 | 0.29687 | -- |
SUPER/GLM(Q) | 10 | NC_037552.1 | 112,491,377 | 3.2491 × 10−8 | 0.32257 | ZNF777; ZNF746 |
SUPER/GLM(Q) | 11 | NC_037552.1 | 113,607,118 | 2.4523 × 10−8 | 0.33352 | ABCB8; ASIC3; CDK5; SLC4A2; FASTK; TMUB1; AGAP3 |
SUPER/GLM(Q) | 12 | NC_037553.1 | 15,992,633 | 2.4361 × 10−8 | 0.36112 | FAM81B |
SUPER/GLM(Q) | 13 | NC_037554.1 | 9,287,335 | 9.7346 × 10−8 | 0.31436 | TULP4; GTF2H5; SERAC1 |
SUPER/GLM(Q) | 14 | NC_037554.1 | 16,312,432 | 1.3425 × 10−9 | 0.3879 | -- |
SUPER/GLM(Q) | 15 | NC_037554.1 | 99,978,913 | 1.0129 × 10−7 | 0.33706 | -- |
SUPER/GLM(Q) | 16 | NC_037555.1 | 32,169,042 | 1.5181 × 10−7 | 0.33459 | -- |
SUPER/GLM(Q) | 17 | NC_037556.1 | 75,679,149 | 8.5899 × 10−8 | 0.36278 | -- |
SUPER/GLM(Q) | 18 | NC_037556.1 | 80,488,833 | 1.413 × 10−8 | 0.39141 | KCNS3; MSGN1 |
SUPER/GLM(Q) | 19 | NC_037556.1 | 81,118,534 | 7.4243 × 10−9 | 0.36956 | -- |
SUPER/GLM(Q) | 20 | NC_037558.1 | 8,094,566 | 8.613 × 10−8 | 0.37056 | YBX1; SLC2A10 |
SUPER/GLM(Q) | 21 | NC_037559.1 | 57,471,045 | 5.8845 × 10−8 | 0.32884 | -- |
SUPER/GLM(Q) | 22 | NC_037559.1 | 74,176,040 | 3.5625 × 10−8 | 0.35173 | WISP1; NDRG1 |
SUPER/GLM(Q) | 23 | NC_037561.1 | 25,915,631 | 2.8368 × 10−9 | 0.40653 | -- |
SUPER/GLM(Q) | 24 | NC_037561.1 | 25,915,784 | 1.0496 × 10−9 | 0.40948 | -- |
SUPER/GLM(Q) | 25 | NC_037562.1 | 28,221,520 | 6.038 × 10−8 | 0.34565 | -- |
SUPER/GLM(Q) | 26 | NC_037562.1 | 28,221,526 | 6.038 × 10−8 | 0.34565 | -- |
SUPER/GLM(Q) | 27 | NC_037562.1 | 28,221,527 | 6.038 × 10−8 | 0.34565 | -- |
SUPER/GLM(Q) | 28 | NC_037562.1 | 39,920,231 | 2.277 × 10−9 | 0.40894 | HYDIN |
SUPER/GLM(Q) | 29 | NC_037563.1 | 45,012,914 | 1.8896 × 10−8 | 0.36036 | -- |
SUPER/GLM(Q) | 30 | NC_037564.1 | 36,725,181 | 9.3193 × 10−8 | 0.31929 | LINGO1 |
SUPER/GLM(Q) | 31 | NC_037566.1 | 36,784,161 | 4.9686 × 10−8 | 0.3255 | B4GALT6 |
SUPER/GLM(Q) | 32 | NC_037568.1 | 13,951,865 | 6.9031 × 10−8 | 0.33258 | CALN1 |
SUPER/GLM(Q) | 33 | NC_037569.1 | 5,832,499 | 2.107 × 10−8 | 0.35009 | KAL1 |
SUPER/GLM(Q) | 34 | NC_037569.1 | 38,961,581 | 1.0446 × 10−7 | 0.29241 | BCOR |
Candidate Gene | SNP (Chr:Pos) | Calving Interval (Year) | ||
---|---|---|---|---|
Homozygous Mutation | Heterozygous Mutation | Reference Genotype | ||
GRM1 | NC_037554.1:20660384 | A/A | G/A | G/G |
1.02 ± 0.15 B | 1.21 ± 0.23 B | 1.52 ± 0.28 A |
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Li, W.; Zheng, H.; Cao, D.; Duan, A.; Huang, L.; Feng, C.; Yang, C. GRM1 as a Candidate Gene for Buffalo Fertility: Insights from Genome-Wide Association Studies and Its Role in the FOXO Signaling Pathway. Genes 2025, 16, 193. https://doi.org/10.3390/genes16020193
Li W, Zheng H, Cao D, Duan A, Huang L, Feng C, Yang C. GRM1 as a Candidate Gene for Buffalo Fertility: Insights from Genome-Wide Association Studies and Its Role in the FOXO Signaling Pathway. Genes. 2025; 16(2):193. https://doi.org/10.3390/genes16020193
Chicago/Turabian StyleLi, Wangchang, Haiying Zheng, Duming Cao, Anqin Duan, Liqing Huang, Chao Feng, and Chunyan Yang. 2025. "GRM1 as a Candidate Gene for Buffalo Fertility: Insights from Genome-Wide Association Studies and Its Role in the FOXO Signaling Pathway" Genes 16, no. 2: 193. https://doi.org/10.3390/genes16020193
APA StyleLi, W., Zheng, H., Cao, D., Duan, A., Huang, L., Feng, C., & Yang, C. (2025). GRM1 as a Candidate Gene for Buffalo Fertility: Insights from Genome-Wide Association Studies and Its Role in the FOXO Signaling Pathway. Genes, 16(2), 193. https://doi.org/10.3390/genes16020193