Table 8 GWAS validation results for udder traits in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) cows
QTL IDa | BTA | Breed | Traits (# QTLb) | Candidate variantsc | 50K SNPs | Variant with the most significant effect | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
# Total | # with -log10(P) > 6 | # in TOP10 | Best rank | Total# | # with -log10(P) > 6 | # in TOP10 | Best rank | Position (pb) | ID | − log10(P) | Functional annotation | ||||
37 | 1 | HOL | US(1) | 4 | 2 | 4 | 1 | 11 | 0 | 6 | 3 | 110,870,166 | rs42324415 | 6.8 | Intergenic |
38 | 2 | NOR | RUH(4) | 14 | 0 | 2 | 1 | 80 | 0 | 8 | 2 | 6,325,829 | rs385535384 | 3.0 | Intergenic |
39 | 4 | HOL | UD(1) | 0 | 0 | 0 | 0 | 3 | 0 | 3 | 1 | 10,078,207 | rs42524753 | 1.7 | Intergenic |
40 | 4 | HOL | FTD(1) | 5 | 0 | 5 | 3 | 2 | 0 | 2 | 1 | 70,680,040 | rs41652994 | 1.0 | Intergenic |
41 | 5 | HOL | TL(1) | 5 | 4 | 5 | 2 | 3 | 1 | 3 | 1 | 12,443,146 | rs41604034 | 10.7 | TMTC2 intron |
42 | 5 | HOL | UD(1) | 17 | 8 | 9 | 1 | 3 | 1 | 1 | 4 | 88,812,245 | rs209585944 | 16.9 | ABCC9 intron |
42 | 5 | HOL | FUA(1) | 17 | 8 | 9 | 1 | 3 | 1 | 1 | 3 | 88,812,245 | rs209585944 | 17.6 | ABCC9 intron |
43 | 6 | HOL | RUH(1) | 0 | 0 | 0 | 0 | 18 | 0 | 7 | 1 | 72,028,756 | rs110103615 | 3.8 | Intergenic |
44 | 6 | MON | UD(1) | 20 | 17 | 8 | 1 | 7 | 0 | 2 | 7 | 88,723,742 | rs436532576 | 19.1 | GC intron |
45 | 6 | HOL | SCS(1) | 37 | 6 | 10 | 1 | 14 | 3 | 0 | 18 | 88,723,742 | rs436532576 | 6.3 | GC intron |
45 | 6 | HOL | UD(1) | 37 | 22 | 10 | 1 | 19 | 0 | 0 | 18 | 88,723,742 | rs436532576 | 19.4 | GC intron |
46 | 8 | HOL | FTD(2) | 4 | 0 | 3 | 3 | 19 | 0 | 7 | 1 | 83,693,221 | rs41570498 | 3.5 | Intergenic |
47 | 9 | MON | SCS(1) | 2 | 0 | 2 | 2 | 12 | 0 | 5 | 1 | 23,517,815 | rs41611219 | 2.7 | ME1 intron |
48 | 9 | MON | SCS(1) | 1 | 0 | 1 | 7 | 12 | 5 | 9 | 1 | 25,793,691 | rs109661188 | 0.3 | NCOA7 intron |
49 | 9 | MON | SCS(1) | 1 | 0 | 1 | 1 | 13 | 0 | 9 | 2 | 29,130,097 | . | 0.8 | HSF2 missense |
50 | 14 | MON | RUH(1) | 24 | 12 | 10 | 1 | 17 | 0 | 0 | 12 | 25,015,640 | rs109815800 | 29.5 | PLAG1 intron |
51 | 17 | MON | FUA(1) | 3 | 0 | 3 | 1 | 60 | 0 | 2 | 4 | 62,695,902 | rs109014048 | 5.9 | Intergenic |
51 | 17 | MON | US(1) | 9 | 8 | 9 | 1 | 6 | 0 | 1 | 10 | 62,809,661 | rs110701343 | 6.9 | Intergenic |
52 | 17 | NOR | US(1) | 10 | 5 | 8 | 1 | 5 | 0 | 2 | 6 | 62,693,355 | rs109184112 | 14.7 | Intergenic |
53 | 19 | HOL | MSS(1) | 12 | 12 | 9 | 1 | 11 | 0 | 1 | 9 | 7,543,195 | rs109941836 | 8.5 | Intergenic |
54 | 19 | HOL | MSS(1) | 11 | 0 | 2 | 3 | 18 | 0 | 8 | 1 | 60,009,650 | rs41653204 | 3.3 | Intergenic |
55 | 19 | MON | UD(1) | 4 | 0 | 4 | 3 | 6 | 1 | 6 | 1 | 61,478,388 | rs109108437 | 5.4 | Intergenic |
55 | 19 | MON | MSS(1) | 10 | 0 | 7 | 3 | 2 | 0 | 3 | 1 | 59,984,238 | rs110395313 | 3.1 | Intergenic |
56 | 20 | HOL | FUA(3) | 13 | 4 | 4 | 1 | 5 | 0 | 6 | 2 | 27,756,459 | rs382512825 | 10.1 | ISL1 upstream |
57 | 24 | MON | UB(1) | 13 | 8 | 8 | 1 | 8 | 2 | 2 | 9 | 34,317,850 | rs210449055 | 13.7 | Intergenic |
58 | 24 | HOL | RUH(1) | 17 | 0 | 9 | 1 | 5 | 1 | 1 | 5 | 34,317,850 | rs210449055 | 2.7 | Intergenic |
59 | 26 | HOL | TO(1) | 8 | 8 | 8 | 1 | 26 | 0 | 2 | 9 | 38,617,279 | rs109011767 | 10.7 | RAB11FIP2 3′ UTR |
60 | 28 | MON | MSS(1) | 2 | 0 | 1 | 3 | 15 | 1 | 9 | 1 | 20,014,813 | rs42137452 | 2.2 | Intergenic |
61 | 29 | HOL | UD(3) | 20 | 0 | 2 | 3 | 27 | 0 | 8 | 1 | 49,412,703 | rs42194458 | 1.9 | KCNQ1 intron |
61 | 29 | HOL | SCS(1) | 11 | 0 | 4 | 1 | 25 | 5 | 6 | 2 | 50,066,017 | rs133306466 | 2.2 | IGF2 downstream |
61 | 29 | HOL | UB(2) | 23 | 0 | 6 | 2 | 43 | 0 | 4 | 1 | 50,296,573 | rs42196507 | 2.8 | SYT8 upstream |