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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)