Table 5.
Genome-wide eQTL for 497 candidate genes expressed in the gluteus medius (GM) muscle of Duroc pigs
| Ensembl ID | SSC | N | SNP | Region (Mb) | q-value | B | δ ± SE | A1 | MAF |
|---|---|---|---|---|---|---|---|---|---|
| ENSSSCG00000004064 | 1 | 27 | rs81289665 | 5.69–10.57 | 4.34E−03 | 1.30E−02 | − 0.45 ± 0.09 | G | 0.42 |
| ENSSSCG00000004071 | 1 | 6 | rs81278169 | 12.26–13.05 | 8.75E−04 | 8.75E−04 | 0.51 ± 0.09 | A | 0.40 |
| ENSSSCG00000014432 | 2 | 1 | rs80929229 | 149.45–149.45 | 3.71E−03 | 2.97E−02 | − 0.47 ± 0.10 | A | 0.10 |
| ENSSSCG00000014432 | 2 | 9 | rs81290831 | 150.27–151.35 | 2.72E−03 | 1.91E−02 | − 0.46 ± 0.09 | A | 0.11 |
| ENSSSCG00000005976 | 4 | 6 | rs80965603 | 14.33–15.13 | 1.55E−02 | 3.10E−02 | 0.24 ± 0.05 | C | 0.28 |
| ENSSSCG00000005976 | 4 | 1 | rs81261174 | 29.68–29.68 | 4.40E−02 | 3.08E−01 | 0.23 ± 0.05 | C | 0.29 |
| ENSSSCG00000032907 | 4 | 3 | rs80955389 | 89.79–89.95 | 4.01E−02 | 1.00E+00 | − 0.24 ± 0.06 | C | 0.48 |
| ENSSSCG00000032907 | 4 | 32 | rs80977488 | 90.00–99.43 | 4.25E−04 | 4.25E−04 | 0.35 ± 0.06 | G | 0.36 |
| ENSSSCG00000032907 | 4 | 4 | rs80889119 | 103.32–103.47 | 4.01E−02 | 1.00E+00 | 0.31 ± 0.08 | G | 0.45 |
| ENSSSCG00000033497 | 6 | 4 | rs81388022 | 68.99–69.13 | 1.85E−02 | 7.41E−02 | 0.34 ± 0.07 | C | 0.23 |
| ENSSSCG00000027659 | 6 | 25 | rs81389074 | 80.81–82.56 | 8.02E−04 | 1.36E−02 | − 0.30 ± 0.06 | A | 0.15 |
| ENSSSCG00000038994 | 6 | 19 | rs81389074 | 80.81–82.15 | 6.32E−03 | 1.14E−01 | 0.85 ± 0.18 | A | 0.15 |
| ENSSSCG00000027659 | 6 | 2 | rs81309503 | 111.39–111.40 | 3.98E−02 | 1.00E+00 | − 0.26 ± 0.06 | G | 0.15 |
| ENSSSCG00000025087 | 6 | 2 | rs81393449 | 156.12–156.13 | 4.27E−02 | 8.55E−02 | − 0.42 ± 0.09 | A | 0.09 |
| ENSSSCG00000003844 | 6 | 3 | rs81345502 | 157.59–158.65 | 1.13E−06 | 1.13E−06 | 0.30 ± 0.05 | G | 0.43 |
| ENSSSCG00000003844 | 6 | 1 | rs81333128 | 162.74–162.74 | 2.37E−02 | 7.10E−02 | 0.21 ± 0.04 | A | 0.34 |
| ENSSSCG00000001455 | 7 | 12 | rs339209635 | 23.40–26.06 | 9.64E−03 | 1.98E−02 | 0.60 ± 0.12 | A | 0.49 |
| ENSSSCG00000024596 | 8 | 1 | rs81237638 | 37.96–37.96 | 1.60E−02 | 6.55E−01 | − 0.33 ± 0.08 | G | 0.33 |
| ENSSSCG00000024596 | 8 | 22 | rs81402024 | 83.19–89.67 | 1.58E−02 | 1.23E−01 | − 0.37 ± 0.08 | C | 0.37 |
| ENSSSCG00000024596 | 8 | 39 | rs81402439 | 90.31–99.95 | 1.58E−02 | 2.99E−01 | 0.34 ± 0.08 | G | 0.33 |
| ENSSSCG00000024596 | 8 | 11 | rs81310686 | 100.02–101.17 | 1.58E−02 | 4.81E−01 | 0.34 ± 0.08 | A | 0.31 |
| ENSSSCG00000024596 | 9 | 1 | rs81420190 | 14.32–14.32 | 4.59E−02 | 1.00E+00 | − 0.30 ± 0.08 | C | 0.24 |
| ENSSSCG00000015129 | 9 | 4 | rs81408352 | 24.50–28.89 | 6.62E−03 | 1.28E−01 | − 0.27 ± 0.06 | G | 0.10 |
| ENSSSCG00000015129 | 9 | 28 | rs81318704 | 35.15–39.98 | 6.62E−03 | 1.39E−01 | − 0.25 ± 0.06 | A | 0.12 |
| ENSSSCG00000015129 | 9 | 10 | rs81410722 | 45.90–47.65 | 2.64E−05 | 5.28E−05 | − 0.25 ± 0.04 | G | 0.17 |
| ENSSSCG00000015129 | 9 | 3 | rs81226448 | 54.24–54.49 | 2.97E−02 | 7.72E−01 | − 0.15 ± 0.03 | C | 0.28 |
| ENSSSCG00000015129 | 9 | 1 | rs81412811 | 65.10–65.10 | 4.49E−02 | 1.00E+00 | − 0.19 ± 0.05 | C | 0.12 |
| ENSSSCG00000017895 | 12 | 9 | rs81436670 | 50.91–53.86 | 4.50E−07 | 1.36E−06 | 0.40 ± 0.06 | G | 0.33 |
| ENSSSCG00000023829 | 14 | 1 | rs80875259 | 31.27–31.27 | 1.24E−06 | 3.74E−02 | − 0.36 ± 0.07 | G | 0.42 |
| ENSSSCG00000014791 | 17 | 1 | rs81466737 | 47.44–47.44 | 9.17E−07 | 2.76E−02 | 0.33 ± 0.07 | A | 0.22 |
SSC, Sus scrofa chromosome; N, number of SNPs significantly associated with the gene under study; SNP, corresponds to the most significant associated SNP; Region (Mb), region containing the SNPs significantly associated with the gene under study; P-value, nominal P-value of association between gene expression and SNP; q-value, q-value calculated with a false discovery rate approach; B, Bonferroni corrected P-values; δ, effect size of the marker and its standard error (SE); A1, minor allele; MAF, minor allele frequency