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Table 8 Candidate genes identified by listed variants in coding or regulatory regions with a posterior probability ≥ 0.25 for Milk, Protein or Fat Yield (AUS BayesRC Lact)

From: Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

Gene_ID (see names in Table 9) DEa Milk Y Prot.Y Fat Y P% F% Evidenceb Variant type (distance from gene or SIFT prediction) Variant position (chrom : bp)
ROBO1 n   + +    P upstream (1823 bp) 1:26212317
SLC37A1 ++ +      L,D downstream (4005 bp) 1:144441230
PSMB2 n -   -    P,L missense (SIFT:deleterious) 3:110752811
OGDH n + +     P downstream (4105 bp) 4:77454411
MYH9 n + +     P,L upstream (1635 bp) 5:75181544
NCF4 n +    - - P,L,V missense (SIFT:tolerated) 5:75659419
ARNTL2 n - -     P upstream (3413 bp) 5:82942569
MGST1 + +   -   - P,V,D upstream (4589 bp)
intron
5:93954751
5:93945655
CSN2 ++++   +     L,V,D intron 6:87180731
CSN3 ++++   -   -   P,L,D missense (SIFT:tolerated)
upstream (2036 bp)
6:87390576
6:87376362
GC n + +   - - P,L,V upstream (2582 bp) 6:88741762
RDH8 n -      L missense (SIFT:deleterious) 7:15815974
TTC7B +    +    D downstream (3086 bp) 10:103182221
PROM2 ++ -      D missense (SIFT:tolerated) 11:2003275
PAEP ++++ + +    - P,L,V,D missense (SIFT:tolerated) 11:103303475
ABO ++   +     L,D downstream (2688 bp) 11:104229609
DGAT1 n + + - - - P,L,V intron
missense (SIFT:tolerated)
14:1801116
14:1802266
COX6C n   + +    P,L downstream (1091 bp)
downstream (3684 bp)
14:66648812
14:66651404
TRIM29 +++ -     + P, D downstream (658 bp) 15:31212485
KRT19 +++ -   -    P,L,D missense (SIFT:tolerated) 19:42366926
PTRF + - -     P,D upstream (4742 bp) 19:43166907
ERGIC1 ++ -      L,D intron 20:4543452
GHR + +      D,V downstream (4947 bp) 20:31885789
SMEK1 n + +    - P,V downstream (2777 bp) 21:56798101
WARS + - -     P,L,D intron 21:66916247
MLH1 n -      L,V synonymous 22:10493668
GMDS + +      D intron 23:51280200
MARF1 n + +     P downstream (24 bp) 25:14138518
SCD +++    +    D downstream (1134 bp) 26:21140458
PRDX3 n   - -    P,L upstream (3744 bp) 26:39685136
  1. The relative direction of the variant effect on milk traits is shown as ‘+’ or ‘-‘. The direction of effects for fat and protein percent (F%, P%) are included if their posterior probability was > 0.2 (AUS BayesRC Lact) as further validation of the Yield traits
  2. aThe strength of RNAseq differential gene expression in lactating mammary tissue compared to 17 other body tissues [22]. Differential expression is indicated if log2 fold change (LFC) > 1 (ie. >21 increase in expression) and p-value < 1.0e-4 and “n” indicates no differential expression. The strength of expression is indicated as + for a LFC value between 1 to 2, ++ for 2 to 5, +++ for 5 to10 and ++++ for above 10
  3. bEvidence for candidate genes included one or more of the following: a member of the Lact gene set (L), associated with more than one milk trait (P), differentially expressed in mammary tissue (D), and/or validated in the DANZ analysis (V)