Table 2 Top SNPs and candidate genes associated with hypocalcemia (CALC), displaced abomasum (DSAB), ketosis (KETO), mastitis (MAST), metritis (METR), retained placenta (RETP) and cow livability
From: GWAS and fine-mapping of livability and six disease traits in Holstein cattle
Trait | Chr | Position | MAF | P-value | Genes Nearby | Traits Previously Associatedb |
|---|---|---|---|---|---|---|
CALC | 6 | 10,521,824 | 0.014 | 8.3 × 10−10a | TRAM1L1, NDST4 | Subcutaneous fat |
DSAB | 4 | 97,101,981 | 0.021 | 4.4 × 10−7 | PLXNA4, CHCHD3 | Milk protein yield |
DSAB | 8 | 83,052,202 | 0.109 | 1.3 × 10−7 | FANCC | Stature |
DSAB | 29 | 35,977,236 | 0.073 | 1.3 × 10−7 | NTM | Milk kappa-casein percentage |
KETO | 14 | 2,762,595 | 0.033 | 1.8 × 10− 9a | LY6K | Milk protein percentage |
KETO | 16 | 7,048,452 | 0.019 | 1.9 × 10−8 | KCNT2 | Milk fat percentage |
MAST | 6 | 88,868,886 | 0.460 | 4.2 × 10−8 | GC | Clinical mastitis |
METR | 4 | 3,662,486 | 0.011 | 2.7 × 10−7 | RF00322 | Milk protein yield |
RETP | 4 | 32,578,298 | 0.218 | 7.4 × 10−7 | RUNDC3B | Calving ease |
RETP | 6 | 117,620,548 | 0.026 | 7.2 × 10−7 | QDPR | Milk kappa-casein percentage |
RETP | 11 | 7,465,110 | 0.060 | 9.1 × 10− 8 | TMEM182 | Abomasum displacement |
RETP | 18 | 64,492,219 | 0.012 | 1.6 × 10−7 | ZFP28 | Still birth |
Livability | 5 | 88,823,164 | 0.472 | 1.5 × 10−10a | ABCC9 | Productive life |
Livability | 6 | 88,801,999 | 0.454 | 1.7 × 10−18a | GC | Clinical mastitis |
Livability | 14 | 8,536,538 | 0.020 | 5.3 × 10−10a | ZFAT | Productive life |
Livability | 18 | 58,194,319 | 0.075 | 1.1 × 10−20a | ZNF614 | Bovine respiratory disease |
Livability | 21 | 56,700,449 | 0.013 | 8.6 × 10−11a | CCDC88C | Type |
Livability | 23 | 26,131,593 | 0.017 | 3.8 × 10−9a | BLA-DQB | Antibody-mediated immune response |