Table 1.
Tibetan pigs-specific single nucleotide polymorphisms in regulatory and/or coding regions harbored by differentially expressed genes related to skeletal muscle development
| Chrom | Position | SNP type | Gene name | Ref allele | Alt allele | Allele frequency of Alt allele | |
|---|---|---|---|---|---|---|---|
|
| |||||||
| TIBP | LWP | ||||||
| 1 | 240,842,119 | Upstream | TGFBR1 | C | T | 0.81 | 0.00 |
| 2 | 5,208,908 | Upstream | GRK2 | T | C | 0.83 | 0.00 |
| 2 | 5,208,922 | Upstream | GRK2 | T | C | 0.82 | 0.00 |
| 2 | 5,208,923 | Upstream | GRK2 | G | A | 0.82 | 0.00 |
| 3 | 118,010,986 | 3′ Prime UTR | SDC1 | G | A | 0.81 | 0.00 |
| 4 | 115,749,645 | Synonymous | COL11A1 | C | T | 0.93 | 0.00 |
| 5 | 100,755,208 | Synonymous | MYF5 | C | G | 0.84 | 0.00 |
| 7 | 115,249,986 | Upstream | ASB2 | A | G | 0.90 | 0.00 |
| 7 | 115,250,009 | Upstream | ASB2 | A | G | 0.90 | 0.00 |
| 7 | 115,250,023 | Upstream | ASB2 | G | A | 0.89 | 0.00 |
| 7 | 115,250,304 | Upstream | ASB2 | A | G | 0.86 | 0.00 |
| 7 | 115,250,849 | Upstream | ASB2 | A | G | 0.90 | 0.00 |
| 7 | 115,250,890 | Upstream | ASB2 | A | C | 0.88 | 0.00 |
| 7 | 115,250,903 | Upstream | ASB2 | T | C | 0.89 | 0.00 |
| 8 | 40,994,493 | Synonymous | PDGFRA | T | C | 0.99 | 0.00 |
| 8 | 40,994,827 | Synonymous | PDGFRA | C | T | 0.87 | 0.00 |
| 8 | 41,009,677 | Synonymous | PDGFRA | T | C | 0.94 | 0.00 |
| 8 | 81,210,043 | Upstream | EDNRA | A | G | 1.00 | 0.00 |
| 8 | 81,277,681 | Upstream | EDNRA | A | G | 0.89 | 0.00 |
| 8 | 81,278,079 | Upstream | EDNRA | A | T | 0.83 | 0.00 |
| 9 | 45,468,105 | Upstream | SCN4B | T | C | 0.89 | 0.00 |
| 9 | 45,468,285 | Upstream | SCN4B | T | C | 0.90 | 0.00 |
| 9 | 45,468,683 | Upstream | SCN4B | T | C | 0.88 | 0.00 |
| 10 | 8,436,053 | Downstream | TGFB2 | T | G | 0.81 | 0.00 |
| 10 | 23,568,482 | Upstream | CACNA1S | G | C | 0.95 | 0.00 |
| 12 | 16,774,572 | Upstream | MYL4 | G | A | 0.93 | 0.00 |
| 13 | 205,937,377 | Upstream | PDE9A | T | C | 0.83 | 0.00 |
| 13 | 205,997,808 | Upstream | PDE9A | T | C | 0.84 | 0.00 |
| 13 | 206,000,181 | 5′ Prime UTR | PDE9A | T | C | 0.86 | 0.00 |
| 13 | 206,000,259 | 5′ Prime UTR | PDE9A | T | C | 0.84 | 0.00 |
| 13 | 206,033,545 | Missense | PDE9A | T | G | 0.87 | 0.00 |
| 13 | 206,034,864 | 3′ Prime UTR | PDE9A | T | C | 0.89 | 0.00 |
| 14 | 10,494,0521 | Upstream | MYOF | A | C | 0.87 | 0.00 |
| 15 | 33,537,058 | Splice region & intron | MYOM2 | G | A | 0.86 | 0.00 |
| 15 | 64,749,414 | Upstream | ACVR1 | T | A | 0.92 | 0.00 |
| 15 | 64,750,217 | 3′ Prime UTR | ACVR1 | T | A | 0.92 | 0.00 |
| 15 | 64,750,438 | 3′ Prime UTR | ACVR1 | T | C | 0.94 | 0.00 |
| 15 | 64,756,963 | 3′ Prime UTR | ACVR1 | G | A | 0.93 | 0.00 |
| 15 | 64,824,052 | Upstream | ACVR1 | A | G | 0.80 | 0.00 |
| 16 | 38,183,547 | 5′ Prime UTR | PDE4D | T | C | 0.93 | 0.00 |
| 18 | 48,694,221 | 5′ Prime UTR premature start codon gain | PGAM2 | G | A | 0.83 | 0.00 |
| 18 | 48,694,249 | 5′ Prime UTR | PGAM2 | A | G | 0.86 | 0.00 |
| 18 | 48,694,283 | 5′ Prime UTR | PGAM2 | T | A | 0.82 | 0.00 |
| 19 | 112,597,017 | 3′ Prime UTR | ZIC3 | A | G | 0.97 | 0.00 |
SNPs, single nucleotide polymorphisms; TIBP, Tibetan pig; LWP, Large White pig; UTR, untranslated regions.