Table 2.
Most significantly associated SNP for female fertility traits in the regions selected based on QTL segregating for the fertility index
| BTA20 | |||||||
|---|---|---|---|---|---|---|---|
| Trait name 2 | SNP | MAF | -log 10 (P-value) | Annotation 1 | Ensemble name | Gene name | Gene description |
| FTI | Chr20:24457090 | 0.20 | 11.42 | intergenic_variant | |||
| AISc | Chr20:24457090 | 0.20 | 10.56 | intergenic_variant | |||
| AISh | Chr20:24457090 | 0.20 | 5.99 | intergenic_variant | |||
| ICF | Chr20:24814046 | 0.22 | 12.21 | intergenic_variant | |||
| IFLc | Chr20:24457090 | 0.20 | 11.88 | intergenic_variant | |||
| IFLh | Chr20:24811587 | 0.24 | 8.89 | intergenic_variant | |||
| NRRc | Chr20:24457090 | 0.20 | 7.69 | intergenic_variant | |||
| NRRh | Chr20:24457090 | 0.20 | 5.68 | intergenic_variant | |||
| BTA23 | |||||||
| FTI | Chr23:30817360 | 0.42 | 9.51 | intergenic_variant | |||
| AISc | Chr23:30586684 | 0.38 | 12.43 | missense_variant | ENSBTAG00000005885 | F1N1L2 | Olfactory receptor |
| AISh | Chr23:30634587 | 0.39 | 9.63 | intergenic_variant | |||
| ICF | Chr23:30364272 | 0.02 | 5.82 | intergenic_variant | |||
| IFLc | Chr23:30831993 | 0.47 | 10.75 | downstream_gene_variant | ENSBTAG00000044946 | Novel miRNA | |
| IFLh | Chr23:30634587 | 0.39 | 8.66 | intergenic_variant | |||
| NRRc | Chr23:30090044 | 0.37 | 11.13 | missense_variant | ENSBTAG00000008943 | ZSCAN12 | Bos taurus zinc finger and SCAN domain containing 12 |
| NRRh | Chr23:30602861 | 0.43 | 10.22 | upstream_gene_variant | ENSBTAG00000040307 | F1N7S5 | Olfactory receptor |
| BTA7 | |||||||
| FTI | Chr7:79631927 | 0.07 | 8.98 | intergenic_variant | |||
| AISc | Chr7:78685481 | 0.06 | 5.73 | intergenic_variant | |||
| AISh | Chr7:78685062 | 0.06 | 13.16 | intergenic_variant | |||
| ICF | Chr7:78287019 | 0.07 | 12.3 | intergenic_variant | |||
| IFLc | Chr7:78685481 | 0.06 | 6.54 | intergenic_variant | |||
| IFLh | Chr7:78685481 | 0.06 | 14.86 | intergenic_variant | |||
| NRRc | Chr7:78380148 | 0.08 | 4.28 | intergenic_variant | |||
| NRRh | Chr7:78685062 | 0.06 | 10.50 | intergenic_variant | |||
| BTA9 QTL1 | |||||||
| FTI | Chr9:39070817 | 0.34 | 6.79 | intergenic_variant | |||
| AISc | Chr9:40178726 | 0.48 | 8.22 | intergenic_variant | |||
| AISh | Chr9:39056106 | 0.29 | 10.86 | intergenic_variant | |||
| ICF | Chr9:43897568 | 0.16 | 9.19 | intron_variant | ENSBTAG00000017527 | AIM1 | absent in melanoma 1 |
| IFLc | Chr9:43027665 | 0.30 | 7.12 | intron_variant | ENSBTAG00000019175 | SOBP | sine oculis binding protein homolog (Drosophila) |
| IFLh | Chr9:40147543 | 0.47 | 8.30 | intergenic_variant | |||
| NRRc | Chr9:40176331 | 0.48 | 7.59 | intergenic_variant | |||
| NRRh | Chr9:39056106 | 0.29 | 8.37 | intergenic_variant | |||
| BTA9 QTL2 | |||||||
| FTI | Chr9:103675274 | 0.14 | 9.01 | intergenic_variant | |||
| AISc | Chr9:102992258 | 0.37 | 7.52 | intron_variant | ENSBTAG00000021741 | RPS6KA2 | ribosomal protein S6 kinase, 90 kDa, polypeptide 2 |
| AISh | Chr9:103880081 | 0.43 | 9.57 | intron_variant | ENSBTAG00000005557 | MLLT4 | myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 |
| ICF | Chr9:103664731 | 0.14 | 10.66 | intergenic_variant | |||
| IFLc | Chr9:104308602 | 0.44 | 9.45 | intron_variant | ENSBTAG00000013176 | SMOC2 | SPARC related modular calcium binding 2 |
| IFLh | Chr9:103861364 | 0.39 | 12.27 | intron_variant&feature_truncation | ENSBTAG00000005557 | MLLT4 | myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 |
| NRRc | Chr9:103788916 | 0.20 | 4.46 | intergenic_variant | |||
| NRRh | Chr9:103861364 | 0.39 | 9.21 | intron_variant&feature_truncation | ENSBTAG00000005557 | MLLT4 | myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 |
| BTA25 | |||||||
| FTI | Chr25:26810616 | 0.27 | 9.37 | upstream_gene_variant | ENSBTAG00000031852 | TBC1D10B | TBC1 domain family, member 10B |
| AISc | Chr25:26864302 | 0.39 | 7.40 | downstream_gene_variant | ENSBTAG00000010851 | SEPHS2 | selenophosphate synthetase 2 |
| AISh | Chr25:27783308 | 0.17 | 8.86 | downstream_gene_variant | ENSBTAG00000047734 | C16orf58 | chromosome 16 open reading frame 58 |
| ICF | Chr25:29847729 | 0.39 | 10.27 | intergenic_variant | |||
| IFLc | Chr25:26810616 | 0.27 | 10.77 | upstream_gene_variant | ENSBTAG00000031852 | TBC1D10B | TBC1 domain family, member 10B |
| NRRc | Chr25:27784063 | 0.17 | 6.45 | downstream_gene_variant | ENSBTAG00000047734 | C16orf58 | chromosome 16 open reading frame 58 |
| NRRh | Chr25:27784062 | 0.17 | 7.56 | downstream_gene_variant | ENSBTAG00000047734 | C16orf58 | chromosome 16 open reading frame 58 |
1In case the SNP marker is annotated as a downstream_gene_variant or an upstream_gene_variant the gene closest located to this SNP is listed.
2Fertility index (FTI); number of inseminations per conception in cows (AISc) and heifers (AISh); the length in days of the interval from calving to first insemination in cows (IFC); days from first to last insemination in cows (IFLc) and heifers (IFLh) and 56-day non-return rate in cows (NRRc) and heifers (NRRh).