Table 4 List of candidate genes with highest posterior probability of causality (PPC) and their minimum P-values for casualty (M_Causality) and GWAS (M_GWAS) associated with hypocalcemia (CALC), displaced abomasum (DSAB), ketosis (KETO), mastitis (MAST), metritis (METR), retained placenta (RETP) and cow livability and their tissue specific expression
From: GWAS and fine-mapping of livability and six disease traits in Holstein cattle
Trait | Gene | Chr | Start | End | M_GWAS P-value | M_Casualty P-value | PPC | Type | Tissue-Specific Expression |
|---|---|---|---|---|---|---|---|---|---|
DSAB | PLXNA4 | 4 | 96,574,369 | 97,120,718 | 4.5 × 10−7 | 6.5 × 10−7 | 0.49 | protein_coding | Aorta, Liver, Trachea |
DSAB | FANCC | 8 | 83,022,522 | 83,228,696 | 1.3 × 10−7 | 2.1 × 10−9 | 0.79 | protein_coding | Thyroid |
DSAB | NTM | 29 | 35,153,012 | 36,117,726 | 1.3 × 10−7 | 1.7 × 10− 7 | 0.99 | protein_coding | Central Nervous System |
LOC107133096 | 14 | 2,760,093 | 2,762,878 | 2.0 × 10−9 | 5.9 × 10−8 | 0.92 | IncRNA | – | |
KETO | PARP10 | 14 | 2,024,509 | 2,031,477 | 7.0 × 10−7 | 1.7 × 10−5 | 0.16 | protein_coding | – |
DGAT1 | 14 | 1,795,425 | 1,804,838 | 1.0 × 10−6 | 1.7 × 10−5 | 0.08 | protein_coding | Bone Marrow | |
KETO | LOC783947 | 16 | 7,050,445 | 7,055,021 | 1.9 × 10−8 | 1.3 × 10−8 | 1.00 | lncRNA | – |
MAST | GC | 6 | 88,687,845 | 88,739,292 | 2.0 × 10−7 | 1.2 × 10−7 | 0.15 | protein_coding | Kidney, Cortex, Liver |
METR | COBL | 4 | 4,494,925 | 4,795,904 | 4.3 × 10−3 | 7.7 × 10−4 | 1.00 | protein_coding | – |
LOC100296627 | 4 | 32,573,079 | 32,613,237 | 7.6 × 10−7 | 4.0 × 10−13 | 1.00 | protein_coding | – | |
RETP | MALSU1 | 4 | 32,051,590 | 32,077,036 | 7.5 × 10−4 | 1,1 × 10−13 | 0.98 | protein_coding | – |
ABCB1 | 4 | 33,013,208 | 33,095,708 | 6.3 × 10−1 | 8.4 × 10−3 | 0.28 | protein_coding | – | |
RETP | TMEM182 | 11 | 7,449,519 | 7,492,871 | 9.0 × 10−8 | 9.9 × 10−8 | 0.96 | protein_coding | Heart, Muscle, Tongue |
RETP | LOC783493 | 18 | 63,799,608 | 63,803,213 | 8.3 × 10−3 | 1.2 × 10−5 | 0.94 | Pseudogene | – |
Livability | ABCC9 | 5 | 8,867,2047 | 88,834,491 | 1.5 × 10−10 | 1.5 × 10−10 | 1.00 | protein_coding | Aorta, Atrium, Lung, Muscle Uterine myometrium, Ventricle |
Livability | GC | 6 | 88,687,845 | 88,739,292 | 1.9 × 10−17 | 1.4 × 10− 19 | 0.03 | protein_coding | Kidney, Cortex, Liver |
Livability | ZFAT | 14 | 8,144,774 | 8,305,775 | 2.1 × 10−5 | 3.2 × 10−5 | 0.23 | protein_coding | – |
Livability | LOC618463 | 18 | 57,587,990 | 57,594,549 | 1.7 × 10−20 | 3.1 × 10−20 | 0.20 | protein_coding | – |
Livability | CCDC88C | 21 | 56,645,629 | 56,773,438 | 8.6 × 10−11 | 8.9 × 10−11 | 0.95 | protein_coding | CD8_cell |
Livability | LOC101908667 | 23 | 25,904,084 | 25,909,461 | 2.1 × 10−8 | 7.9 × 10−9 | 0.31 | lncRNA | – |