TABLE 5.
Positional candidate genes for the top SNP based on percentage of GV explained for each trait.
| Trait a | SNP (% GV) b | Chr c | Gene name d | Description |
|---|---|---|---|---|
| Piglet_T3 | INRA0019871 (11.37%) | 5 | BCL2L13 | BCL2 like 13 |
| BID | BH3 interacting domain death agonist | |||
| MICAL3 | Microtubule associated monooxygenase, calponin and LIM domain containing 3 | |||
| PEX26 | Peroxisomal biogenesis factor 26 | |||
| TUBA8 | Tubulin alpha 8 | |||
| Piglet_T3 | MARC0089811 (3.33%) | 3 | SOX11 | SRY-box transcription factor 11 |
| Piglet_T3 | H3GA0016790 (3.32%) | 5 | BCL2L13 | BCL2 like 13 |
| BID | BH3 interacting domain death agonist | |||
| MICAL3 | Microtubule associated monooxygenase, calponin and LIM domain containing 3 | |||
| PEX26 | Peroxisomal biogenesis factor 26 | |||
| TUBA8 | Tubulin alpha 8 | |||
| USP18 | Ubiquitin specific peptidase 18 | |||
| Fetal_T3 | ALGA0028303 (4.67%) | 4 | None | N/A |
| Fetal_T3 | ALGA0009329 (1.68%) | 1 | HSDL2 | Hydroxysteroid dehydrogenase like 2 |
| PTBP3 | Polypyrimidine tract binding protein 3 | |||
| SUSD1 | Sushi domain containing 1 | |||
| Fetal_T3 | ALGA0119977 (1.26%) | 4 | None | N/A |
| Fetal_T4 | ASGA0057067 (3.51%) | 13 | CCDC12 | Coiled-coil domain containing 12 |
| KIF9 | Kinesin family member 9 | |||
| MYL3 | Myosin light chain 3 | |||
| NBEAL2 | Neurobeachin like 2 | |||
| PTH1R | Parathyroid hormone 1 receptor | |||
| SETD2 | SET domain containing 2, histone lysine methyltransferase | |||
| Fetal_T4 | DIAS0000510 (1.92%) | 15 | ATIC | 5-aminoimidazole-4-carboxamide ribonucleotide Formyltransferase/IMP cyclohydrolase |
| FN1 | Fibronectin 1 | |||
| Fetal_T4 | MARC0052461 (1.54%) | 15 | ARIH2 | Ariadne RBR E3 ubiquitin protein ligase 2 |
| CELSR3 | Cadherin EGF LAG seven-pass G-type receptor 3 | |||
| IP6K2 | Inositol hexakisphosphate kinase 2 | |||
| NCKIPSD | NCK interacting protein with SH3 domain | |||
| PFKFB4 | 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 | |||
| PRKAR2A | Protein kinase cAMP-dependent type II regulatory subunit alpha | |||
| SHISA5 | Shisa family member 5 | |||
| SLC25A20 | Solute carrier family 25 member 20 | |||
| SLC26A6 | Solute carrier family 26 member 6 | |||
| TMEM89 | Transmembrane protein 89 | |||
| U6 | U6 spliceosomal RNA | |||
| UCN2 | Urocortin 2 | |||
| UQCRC1 | Ubiquinol-cytochrome c reductase core protein 1 |
Triiodothyronine (T3) levels were measured in piglet serum at 11 DPI (piglet_T3), in fetal serum at 12 or 21 DPMI (fetal_T3); thyroxine (T4) levels were measured in fetal serum at 12 or 21 DPMI (fetal_T4).
SNP name based on Illumina Porcine SNP60 Beadchip version 2 nomenclature and percent genetic variation (% GV) that was explained by the 1-Mb window for which the SNP was identified as having the highest PPI in the MCMC iterations.
Chromosome (Chr) where a significant window was identified based on Sus scrofa 11.1 (Sscrofa11.1) build.
Gene name based on Ensembl Biomart release 107 with the Pig—Duroc genes (Sscrofa11.1) option accessed on 30 August 2022.