Table 1.
Summary of a selection of sentinel lead SNPs for fatty acid composition and metabolism traits in six pig populations by chromosome regions.
| Chromosome: position |
Trait | Pop | Candidate genes | p-value | MAF (minor/major) |
Var (%)1 | Variant annotation2 |
|---|---|---|---|---|---|---|---|
| 1:8873447 | C18:0 | Bamaxiang | – | 3.02E-08 | 0.30 (A/G) | 11.24 | Intron |
| 2:746298 | ACL | Erhualian | – | 2.31E-08 | 0.07 (G/A) | 17.70 | Upstream |
| 2:8929954 | C20:3n-6/C18:2n-6 | Erhualian | FADS2, FADS1 | 2.90E-22 | 0.43 (C/T) | 25.05 | Intergenic |
| 2:74664653 | C20:3n-6 | F2 | PLIN5 | 1.89E-08 | 0.06 (G/A) | 4.66 | Intergenic |
| 2:115831690 | C20:2n-6 | DLY | – | 5.22E-09 | 0.06 (C/A) | 5.20 | Intergenic |
| 2:145804018 | FattyAI | Bamaxiang | – | 5.09E-09 | 0.38 (T/C) | 12.50 | Intergenic |
| 3:92010559 | C20:1n-9 | Erhualian | – | 9.96E-09 | 0.33 (T/C) | 11.77 | Intergenic |
| 4:63910717 | C18:1n-9/C18:0 | F2 | – | 1.69E-10 | 0.14 (A/G) | 9.49 | Intron |
| 4:86701762 | C20:2n-6 | F2 | – | 6.22E-09 | 0.42 (G/T) | 9.30 | Intergenic |
| 5:73950290 | C20:0/C18:0 | Sutai | ABCD2 | 2.24E-11 | 0.25 (A/G) | 10.75 | Intron |
| 6:67864540 | C20:3n-6 | Sutai | – | 2.52E-08 | 0.27 (T/G) | 7.54 | Intergenic |
| 6:71008471 | C16:1n-7/C16:0 | Laiwu | – | 2.96E-08 | 0.45 (G/T) | 5.61 | Intergenic |
| 7:27337970 | C18:1n-9/C16:1n-7 | Laiwu | APOM | 4.15E-09 | 0.35 (C/T) | 9.13 | Intergenic |
| 7:30614484 | C18:1n-9/C16:1n-7 | Bamaxiang | – | 3.40E-09 | 0.12 (C/T) | 11.85 | Upstream |
| 7:34919339 | n-3 | F2 | – | 4.93E-15 | 0.48 (A/G) | 15.04 | Intron |
| 7:52837555 | C20:1n-9 | Bamaxiang | ACSBG1 | 8.21E-10 | 0.24 (G/A) | 11.69 | Intergenic |
| 7:58228023 | C20:2n-6/C18:2n-6 | Laiwu | – | 1.52E-10 | 0.35 (C/A) | 19.97 | Intergenic |
| 7:134678195 | C20:1n-9/C18:1n-9 | Erhualian | ELOVL5 | 1.07E-23 | 0.22 (G/T) | 34.48 | Intergenic |
| 8:119726275 | C18:1n-9/C16:1n-7 | DLY | ELOVL6 | 1.90E-18 | 0.06 (T/C) | 13.06 | Intergenic |
| 8:129588470 | ACL | DLY | MTTP | 1.64E-08 | 0.12 (G/A) | 6.35 | Intergenic |
| 8:138708016 | C20:4n-6/C20:2n-6 | Bamaxiang | SNCA | 3.14E-08 | 0.06 (A/G) | 9.13 | Intron |
| 9:11302313 | C20:4n-6/C20:3n-6 | Erhualian | DGAT2 | 3.13E-08 | 0.07 (G/A) | 7.30 | Intron |
| 9:13950534 | C16:0/C14:0 | Laiwu | THRSP | 2.91E-08 | 0.10 (T/C) | 17.00 | Intron |
| 12:1176481 | C18:1n-9/C16:1n-7 | Erhualian | FASN | 2.38E-30 | 0.07 (T/C) | 40.86 | Intergenic |
| 12:59707351 | SFA | Laiwu | – | 1.45E-10 | 0.33 (T/C) | 11.23 | Intergenic |
| 13:24928872 | C20:1n-9/C20:0 | Sutai | ACAA1 | 1.14E-09 | 0.16 (C/T) | 15.95 | Intron |
| 13:40365857 | ACL | Bamaxiang | ACOX2 | 4.00E-09 | 0.38 (T/G) | 11.35 | Intergenic |
| 13:165434306 | C20:1n-9 | Sutai | – | 3.62E-08 | 0.07 (A/G) | 11.79 | Intergenic |
| 14:121454019 | C18:0 | DLY | SCD | 3.14E-33 | 0.33 (T/G) | 28.20 | Intergenic |
| 15:146109641 | C20:0 | Laiwu | – | 3.26E-09 | 0.42 (C/T) | 10.01 | Intergenic |
| 16:34617582 | C20:1n-9/C20:0 | Sutai | – | 2.45E-08 | 0.30 (G/A) | 16.65 | Intergenic |
| 16:36821647 | C20:0/C18:0 | Laiwu | – | 1.80E-22 | 0.09 (T/G) | 35.98 | Upstream |
| 16:41393886 | C20:0/C18:0 | F2 | ELOVL7 | 3.94E-44 | 0.29 (A/G) | 36.26 | Intergenic |
| 16:43497948 | C20:0/C18:0 | DLY | ELOVL7 | 3.66E-62 | 0.12 (A/T) | 43.50 | Intergenic |
| 16:48557856 | C20:1n-9/C20:0 | Bamaxiang | – | 3.10E-11 | 0.38 (G/A) | 17.33 | Intergenic |
| X:96131734 | C14:0 | F2 | – | 8.49E-09 | 0.41 (T/A) | 6.91 | Intergenic |
| X:103467488 | FattyAI | F2 | – | 1.63E-10 | 0.32 (A/C) | 8.04 | Intergenic |
Pop, population; MAF, minor allele frequency. 1Var (%), percentage of phenotypic variation explained by the lead SNP for the most significant trait. 2Variant annotation, variant annotation by Variant Effect Predictor (VEP) supported by Ensemble; “–”, no candidate gene found.