Table 1 The most significant SNP at QTL detected across trait-cat meta-analyses and potential candidate genes
Trait category | BTA | Position (bp) | RefSNP id | Annotation | MAF | P value | N of traits | Candidate gene(s) |
|---|---|---|---|---|---|---|---|---|
Milk production | 5 | 93,945,655 | rs134637616 | Intron | 0.26 | 3.26 × 10− 67 | 5 | MGST1 |
6 | 87,172,459 | rs109761275 | Intergenic | 0.30 | 1.35 × 10− 24 | 2 | Casein genes | |
11 | 103,302,351 | rs110186753 | Intron | 0.33 | 7.47 × 10−16 | 1 | PAEP | |
14 | 2,538,953 | rs109673915 | Intron | 0.20 | 2.29 × 10−26 | 2 | GPIHBP1 | |
16d | 1,588,321 | rs109375222 | Intergenic | 0.41 | 3.07 × 10−8 | 1 | – | |
20 | 29,987,376 | rs133636599 | Intergenic | 0.14 | 2.97 × 10−12 | 2 | GHR | |
27d | 36,274,982 | rs133883836 | Intergenic | 0.23 | 5.91 × 10−10 | 1 | AGPAT6 | |
Body size | 1d | 59,332,879 | rs137415420 | Intron | 0.34 | 5.57 × 10− 10 | 0 | DRD3 |
3 | 120,159,650 | rs42818065 | Intergenic | 0.35 | 2.90 × 10−8 | 0 | – | |
11d | 104,496,081 | rs110574932 | Intron | 0.07 | 5.63 × 10−8 | 0 | DBH | |
26 | 22,133,617 | rs42088986 | Intron | 0.24 | 1.00 × 10−14 | 1 | BTRC | |
Leg conformation | 3 | 120,211,603 | rs109854637 | Intergenic | 0.34 | 1.48 × 10−10 | 0 | – |
13d | 60,593,663 | rs110597649 | Intergenic | 0.16 | 4.13 × 10−13 | 2 | RSPO4 | |
26 | 22,717,514 | rs134127590 | Intergenic | 0.31 | 5.92 × 10−10 | 1 | BTRC | |
Mammary gland morphology | 3 | 120,265,990 | rs136664568 | Downstream gene | 0.33 | 3.44 × 10−12 | 2 | – |
5d | 12,507,199 | rs110171876 | Intron | 0.08 | 7.22 × 10−8 | 0 | TMTC2 | |
6 | 90,631,225 | rs133549245 | Upstream gene | 0.27 | 2.94 × 10−29 | 2 | RASSF6 | |
17 | 62,697,699 | rs137563207 | Intergenic | 0.24 | 2.62 × 10−46 | 9 | TBX5, RBM19 | |
19d | 23,233,071 | rs41584904 | Downstream gene | 0.10 | 4.97 × 10−8 | 0 | PITPNA | |
Body conformation (shared) | 5 | 31,524,629 | rs110940367 | Downstream gene | 0.36 | a1.39 × 10−9 c1.20 × 10−15 | 0 2 | – |
|  | 25 | 1,455,150 | rs133315098 | Intergenic | 0.44 | a2.22 × 10−19 b4.47 × 10− 10 c1.00 × 10− 10 | 6 0 0 | IGFALS |
Fertility | 17d | 70,735,784 | rs136040855 | 3′ UTR | 0.14 | 1.22 × 10−12 | 2 | GAS2L1, ASCC2 |
Calving | 9d | 24,850,498 | rs42227651 | Intergenic | 0.17 | 3.54 × 10−10 | 0 | RSPO3 |
19d | 9,600,700 | rs136348444 | Intron | 0.09 | 7.92 × 10−10 | 1 | – | |
21 | 913,715 | rs108992215 | Intergenic | 0.15 | 5.49 × 10−41 | 2 | MAGEL2 | |
25 | 1,489,008 | rs109557202 | Intron | 0.44 | 1.48 × 10−14 | 3 | IGFALS | |
Growth and carcass quality | 10d | 59,164,533 | rs43636323 | Intergenic | 0.34 | 1.65 × 10−9 | 0 | CYP19A1 |
Milking speed | 6 | 90,443,733 | rs133851432 | Intergenic | 0.26 | 1.96 × 10−12 | 1 | RASSF6 |
|  | 19d | 7,610,453 | rs110598898 | Downstream gene | 0.20 | 4.32 × 10−9 | 1 | – |
Longevity | 20d | 34,160,944 | rs135463978 | Intergenic | 0.26 | 6.43 × 10−8 | 0 | – |
|  | 25 | 1,455,150 | rs133315098 | Intergenic | 0.44 | 8.90 × 10−11 | 1 | IGFALS |