Table 3 Description of the QTL identified in GWAS analyses for the 0/1 or 0/1/2 phenotypes of Normande and Holstein cows
Breed | Phenotype | QTL | BTA | Confidence interval | TOP variant (resistance allele) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Start (bp*) | End (bp*) | Number of significant variants | Number of genes | −log10(P) | ID | bp* | Freq. | Effect | SE | Gene | Functional annotation | ||||
Normande | 0/1 | 1 | 23 | 24,804,034 | 25,602,017 | 7 | 3 | 6.4 | rs134517431 | 25,575,732 | 0.43 | − 0.17 | 0.03 | BOLA-DRB2 | Intron |
Normande | 0/1 | 2 | 23 | 26,952,214 | 27,814,232 | 1 | 26 | 6.4 | rs110031509 | 26,977,608 | 0.37 | − 0.15 | 0.03 | NOTCH4 | Synonymous |
Normande | 0/1 | 3 | 23 | 28,576,812 | 28,671,569 | 7 | 2 | 7.0 | rs208517124 | 28,605,243 | 0.31 | − 0.17 | 0.03 | TRIM15 | Intron |
Normande | 0/1 | 4 | 23 | 32,128,351 | 32,606,331 | 25 | 0 | 6.9 | rs108942026 | 32,551,869 | 0.27 | − 0.17 | 0.03 | – | Intergenic |
Holstein | 0/1 | 1 | 12 | 68,908,056 | 69,745,891 | 268 | 2 | 9.4 | rs378812903 | 69,314,330 | 0.81 | − 0.16 | 0.03 | – | Intergenic |
Holstein | 0/1 | 2 | 12 | 69,774,746 | 71,240,801 | 281 | 1 | 10.8 | rs43161232 | 70,723,087 | 0.88 | − 0.19 | 0.03 | – | Intergenic |
Holstein | 0/1 | 3 | 12 | 72,272,367 | 72,416,273 | 144 | 0 | 8.5 | rs43047348 | 72,351,583 | 0.77 | − 0.15 | 0.03 | – | Intergenic |
Holstein | 0/1 | 4 | 12 | 75,283,615 | 75,380,545 | 6 | 0 | 7.7 | rs43104474 | 75,379,770 | 0.90 | − 0.18 | 0.03 | – | Intergenic |
Holstein | 0/1 | 5 | 12 | 76,760,851 | 77,323,511 | 215 | 1 | 8.5 | rs378568583 | 77,285,189 | 0.76 | − 0.14 | 0.02 | – | Intergenic |
Holstein | 0/1 | 6 | 12 | 79,096,880 | 80,067,268 | 6 | 1 | 7.5 | rs379488452 | 80,064,150 | 0.84 | − 0.14 | 0.03 | UBAC2 | Intron |
Holstein | 0/1 | 7 | 13 | 63,497,960 | 63,506,532 | 20 | 0 | 18.5 | rs109570209 | 63,502,566 | 0.91 | − 0.34 | 0.04 | – | Intergenic |
Holstein | 0/1 | 8 | 23 | 23,529,491 | 23,976,432 | 39 | 1 | 7.1 | rs210372926 | 23,956,987 | 0.34 | − 0.11 | 0.02 | PKHD1 | Intron |
Holstein | 0/1 | 9 | 23 | 25,115,933 | 25,582,101 | 360 | 3 | 8.8 | rs209183236 | 25,181,661 | 0.66 | − 0.12 | 0.02 | ELOVL5 | Intron |
Holstein | 0/1 | 10 | 23 | 26,665,220 | 27,629,951 | 114 | 28 | 8.2 | rs470365293 | 26,733,104 | 0.69 | − 0.17 | 0.03 | ENSBTAG00000023541 | Intron |
Holstein | 0/1 | 11 | 23 | 27,630,248 | 28,817,610 | 13 | 5 | 7.4 | rs109539043 | 28,085,410 | 0.81 | − 0.13 | 0.02 | IER3 | Upstream |
Holstein | 0/1/2 | 1 | 12 | 67,954,912 | 69,097,427 | 31 | 0 | 6.9 | rs110051821 | 68,949,675 | 0.67 | − 0.21 | 0.04 | – | Intergenic |
Holstein | 0/1/2 | 2 | 12 | 69,162,598 | 70,723,087 | 267 | 3 | 8.7 | rs41667085 | 70,127,519 | 0.91 | − 0.28 | 0.05 | ABCC4 | Intron |
Holstein | 0/1/2 | 3 | 12 | 71,239,317 | 71,240,801 | 3 | 0 | 6.7 | rs382007737 | 71,240,801 | 0.74 | − 0.25 | 0.05 | – | Intergenic |
Holstein | 0/1/2 | 4 | 12 | 72,272,367 | 72,415,271 | 125 | 0 | 7.4 | rs463644618 | 72,356,381 | 0.95 | − 0.56 | 0.10 | – | Intergenic |
Holstein | 0/1/2 | 5 | 12 | 76,760,851 | 77,323,511 | 65 | 1 | 7.0 | rs383583316 | 77,253,589 | 0.76 | − 0.17 | 0.03 | – | Intergenic |
Holstein | 0/1/2 | 6 | 13 | 63,497,960 | 63,506,532 | 20 | 0 | 38.1 | rs109570209 | 63,502,566 | 0.91 | − 0.71 | 0.05 | – | Intergenic |
Holstein | 0/1/2 | 7 | 23 | 25,119,808 | 25,602,067 | 456 | 3 | 8.9 | rs210655104 | 25,554,248 | 0.83 | − 0.24 | 0.04 | – | Intergenic |
Holstein | 0/1/2 | 8 | 23 | 26,680,418 | 27,629,951 | 345 | 28 | 9.0 | rs470365293 | 26,733,104 | 0.69 | − 0.26 | 0.04 | ENSBTAG00000023541 | Intron |
Holstein | 0/1/2 | 9 | 23 | 27,759,542 | 28,398,451 | 9 | 3 | 7.4 | rs209284762 | 28,012,299 | 0.84 | − 0.21 | 0.04 | – | Intergenic |