Table 3 QTL regions for conformation traits and the most significant SNP within each region in three pig breeds
From: Genome-wide association study for conformation traits in three Danish pig breeds
Trait | n | Chr | QTL region | Most significant SNP | Candidate genesb | |||
|---|---|---|---|---|---|---|---|---|
Right position (bp) | Left position (bp) | SNPa | P value | Effect size (%) | ||||
Landrace | ||||||||
BACK | 41 | 1 | 63,345,571 | 68,207,754 | rs80850790 | 3.53 × 10−8 | 0.12 | SRSF12, PNRC1 |
|  |  | 1 | 81,835,391 | 105,362,894 | rs81287678 | 1.48 × 10−8 | 0.13 | SLC14A2 |
|  |  | 3 | 117,911,196 | 118,765,898 | rs81258584 | 1.64 × 10−7 | 0.11 | PPM1G |
|  |  | 5 | 67,981,416 | 68,326,348 | rs80985094 | 9.93 × 10−8 | 0.14 | CCND2 |
|  |  | 7 | 36,202,231 | 37,157,566 | rs80828473 | 7.41 × 10−12 | 0.19 | PPARD |
HIND | 25 | 1 | 216,980,027 | 242,984,908 | rs80946156 | 5.21 × 10−8 | 0.13 | RCL1 |
CONF | 104 | 3 | 97,726,517 | 97,741,803 | rs81303888 | 2.72 × 10−7 | 0.11 | LRPPRC |
|  |  | 3 | 117,911,196 | 117,911,196 |  | 2.42 × 10−7 | 0.11 | BRE, ENSSSCG00000026465 |
|  |  | 5 | 67,518,456 | 69,897,370 | rs81384722 | 2.29 × 10−8 | 0.15 | ENSSSCT00000000782 |
|  |  | 6 | 74,354,607 | 84,927,021 | rs81389032 | 1.84 × 10−10 | 0.17 | ENSSSCT00000032147, ENSSSCT00000003913 |
|  |  | 7 | 21,053,530 | 37,812,119 | rs80828473 | 6.28 × 10−11 | 0.18 | PPARD |
|  |  | 7 | 131,126,819 | 131,126,819 | rs81397155 | 6.20 × 10−8 | 0.15 | TDRD9, CEP170B |
|  |  | 12 | 24,812,751 | 26,022,727 | rs81312521 | 3.16 × 10−8 | 0.13 | NGFR |
|  |  | 12 | 46,857,615 | 47,352,945 | rs81435770 | 2.09 × 10−7 | 0.11 | PIPOX |
Yorkshire | ||||||||
FRONT | 2 | 7 | 52,843,780 | 52,860,434 | rs80995679 | 1.27 × 10−6 | 0.09 | CHRNB4, PSMA4 |
BACK | 2 | 6 | 142,725,268 | 142,803,333 | rs81305243 | 1.08 × 10−6 | 0.10 | DAB1 |
HIND | 57 | 1 | 92,766,049 | 101,369,745 |  | 5.66 × 10−8 | 0.12 | RIPPLY2, SNAP91 |
|  |  | 1 | 198,725,106 | 205,843,789 | rs80999532 | 1.41 × 10−9 | 0.15 | TMX1, FRMD6 |
|  |  | 7 | 103,101,452 | 121,513,304 | rs80894106 | 3.36 × 10−8 | 0.12 | VRTN, SYNDIG1L |
CONF | 222 | 1 | 92,766,049 | 92,766,049 |  | 4.99 × 10−12 | 0.20 | RIPPLY2, SNAP91 |
|  |  | 1 | 198,725,106 | 208,707,283 | rs80783847 | 2.42 × 10−13 | 0.22 | ENSSSCT00000005518 |
|  |  | 6 | 41,235,400 | 43,110,092 | rs81395827 | 3.82 × 10−9 | 0.15 | ZNF382 |
|  |  | 7 | 102,881,143 | 103,495,170 | rs80894106 | 3.86 × 10−11 | 0.18 | VRTN, SYNDIG1L |
|  |  | 10 | 18,665,600 | 18,920,852 | rs81309142 | 8.35 × 10−8 | 0.12 | ENSSCG00000030502, ZBTB18 |
|  |  | 12 | 14,208,800 | 15,365,718 | rs81440562 | 5.63 × 10−12 | 0.20 | CD79B, GH1 |
|  |  | 18 | 10,626,879 | 14,885,152 | rs81469271 | 4.39 × 10−9 | 0.15 | ENSSCG000000288580 |
Duroc | ||||||||
FRONT | 12 | 3 | 97,469,056 | 99,288,792 | rs323557679 | 3.28 × 10−7 | 0.16 | MSH2 |
|  |  | 6 | 47,212,157 | 57,685,509 | rs81226413 | 4.22 × 10−8 | 0.18 | ENSSCT00000003685 |
BACK | 128 | 3 | 100,232,086 | 100,448,894 | rs81373717 | 6.41 × 10−31 | 0.85 | EPAS1, PRKCE |
|  |  | 6 | 47,212,157 | 53,526,888 | rs338147539 | 2.59 × 10−8 | 0.19 | CCDC61 |
HIND | 31 | 6 | 54,949,995 | 60,446,765 | rs81327648 | 9.17 × 10−11 | 0.25 | WRAP73 |
CONF | 235 | 2 | 36,580,946 | 46,128,234 |  | 6.01 × 10−8 | 0.16 | ANO3 |
|  |  | 3 | 97,469,056 | 100,477,666 | rs81373756 | 6.44 × 10−20 | 0.54 | PRKCE |
|  |  | 4 | 99,503,615 | 111,556,304 | rs81382406 | 3.88 × 10−8 | 0.17 | CHRNB2 |
|  |  | 6 | 47,573,330 | 57,685,509 | rs81333163 | 5.30 × 10−20 | 0.52 | A1BG, RPS5 |
|  |  | 7 | 34,755,602 | 36,697,937 | rs80852624 | 9.4 × 10−8 | 0.18 | HMGA1, RPS10 |
|  |  | 7 | 103,495,170 | 103,495,170 | rs80894106 | 8.60 × 10−11 | 0.25 | VRTN, SYNDIG1L |
|  |  | 12 | 25,298,982 | 25,580,071 | rs327303574 | 3.80 × 10−11 | 0.26 | ENSSCT00000022825, B4GALNT2 |
|  |  | 13 | 132,640,404 | 133,032,413 |  | 1.21 × 10−6 | 0.14 | IGF2BP2 |