Table 3.
List of SNPs in the Bos taurus autosomes (BTA) showing significant [-log10(P-value) > 4] associations with susceptibility to – (HD) and recoverability (DH) from mastitis.
| Trait∗ | BTA | SNP rsID | α | SEα | -log10P | Nearest gene(s) | Candidate gene | Distance (Kb)∗∗∗ |
|---|---|---|---|---|---|---|---|---|
| HD | 3 | rs109583509 | -0.07 | 0.02 | 4.31 | GRIK3 | GRIK3 | 90112 |
| 7 | rs43732911 | -0.24 | 0.06 | 4.09 | MARCH3 | MARCH3 | Overlap | |
| DH | 7 | rs29012637 | -0.05 | 0.01 | 4.44 | EPS15L1 | EPS15L1 | 79088 |
| 15 | rs110414316 | -0.09 | 0.02 | 5.13 | STARD10, ATG16L2, FCHSD2 | ATG16L2 | Overlap | |
| 15 | rs109344144 | -0.08 | 0.02 | 5.45 | P2RY2, P2RY6, ARHGEF17 | P2RY6 | 4544 | |
| 15 | rs42991413 | -0.09 | 0.02 | 4.31 | ||||
| P1HD | 1 | rs109029759 | -0.10 | 0.03 | 4.20 | PLOD2 | PLOD2 | 269678 |
| 4 | rs110921945 | 0.14 | 0.03 | 4.07 | ENSBTAG00000047979 | ENSBTAG00000047979 | Overlap | |
| 8 | rs109438746 | -0.10 | 0.03 | 4.10 | SCARA3, TMEM215, ENSBTAG00000005574 | SCARA3, ENSBTAG00000005574 | 6358 | |
| 12 | rs41631671 | -0.17 | 0.04 | 4.30 | CYSLTR2, FNDC3A | |||
| P1DH | 15 | rs42550814 | 0.09 | 0.02 | 4.87 | DDI1, PDGFD | PDGFD | Overlap |
| 20 | rs41638346 | 0.15 | 0.04 | 4.08 | IPO11 | IPO11 | 226699 | |
| P2HD | 5 | rs109785134 | 0.15 | 0.03 | 5.21 | STAB2, NT5DC3 | STAB2 | Overlap |
| 6 | rs42639714 | 0.10 | 0.03 | 4.30 | PCDH7 | PCDH7 | 434135 | |
| 9 | rs42574126 | 0.11 | 0.03 | 4.02 | ||||
| P2DH | 1 | rs109126926 | 0.08 | 0.02 | 4.11 | VEPH1, PTX3 | VEPH1, PTX3 | Overlap |
| 6 | rs43317449 | -0.09 | 0.02 | 4.49 | LRIT3, RRH, GAR1, CFI | LRIT3 | 5431 | |
| 6 | rs43453628 | 0.08 | 0.02 | 4.85 | SEC24B, COL25A1 | COL25A1 | 291654 | |
| 13 | rs109674956 | -0.10 | 0.02 | 4.93 | PREX1 | PREX1 | 20117 | |
| 26 | rs41648638 | -0.33 | 0.08 | 4.05 | WDR11 | WDR11 | 112161 | |
| P3HD | 7 | rs41255569 | -0.14 | 0.04 | 4.25 | IFI30, MAST3, ENSBTAG00000002350 | IFI30, MAST3 | 1375 |
| 12 | rs41618899 | 0.12 | 0.03 | 4.04 | FREM2, TRPC4 | FREM2 | 278734 | |
| 13 | rs43150474 | 0.16 | 0.04 | 4.67 | SLX4IP, JAG1 | SLX4IP | Overlap | |
| 13 | rs109036286 | -0.13 | 0.03 | 4.31 | ||||
| 28 | rs29012361 | -0.13 | 0.03 | 4.08 | ||||
| P3DH | 3 | rs41612148 | -0.26 | 0.06 | 5.39 | ENSBTAG00000047248 | ENSBTAG00000047248 | 182592 |
| 3 | rs41626429 | -0.26 | 0.06 | 4.95 | ENSBTAG00000047248 | ENSBTAG00000047248 | 339288 | |
| 5 | rs43145932 | -0.14 | 0.04 | 4.20 | ATXN7L3B | ATXN7L3B | 678832 | |
| 7 | rs41565600 | -0.10 | 0.02 | 4.17 | CSNK1G3 | CSNK1G3 | 271378 | |
∗Trait: HD and DH represent susceptibility to – and recoverability from mastitis all parities analyzed together; P1HD, P2HD, and P3HD = susceptibility to mastitis for parity 1, 2, and 3, respectively; P1DH, P2DH, and P3DH = recoverability from mastitis for parity 1, 2, and 3, respectively.
∗∗The SNP positions in base pairs (bp) were based on the UMD3.1 genome assembly (ftp://ftp.cbcb.umd.edu/pub/data/assembly/Bos_taurus/Bos_taurus_UMD_3.1/).
∗∗∗Distance = physical distance (Kb) from the SNP to the start/end of the nearest candidate gene.