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Table 5 Evaluation of high-impact variants for stallion fertility

From: Screening of whole genome sequences identified high-impact variants for stallion fertility

SNP ID

GENE

EBV-PAT association

GTmissing

2pqhigh

2pqlow

E (q2 stallion)

Number of breeds

Private

Group I

Rare MAF < 0.01

Group II

MAF 0.01-0.1

Group III

MAF >0.1

Group IV

g.26775767G>C

NEURL

     

7

  

+

 

g.77472655G>C

KDR

     

11

   

+

g.74610774C>T

CFTR

 

+

 

0.004

0.001

2

 

+

  

g.56937215C>T

OVGP1

 

+

0.111

 

0.723

3

  

+

 

g.45985131A>G

FBXO43

 

+

 

0.032

0.079

4

  

+

 

g.82699661C>T

TSSK6

 

+

0.068

 

0.355

8

  

+

 

g.7083659A>T

SLC9A3R1

     

12

   

+

g.40694339G>A

PKD1

 

+

 

0.013

0.012

2

 

+

  

g.6704968C>T

GHRL

     

5

  

+

 

g.19034281C>T

FOXP1

 

+

0.111

 

0.861

11

  

+

 

g.32635273T>C

BTNL2

     

7

   

+

g.35255390T>C

TCP11

 

+

 

0.022

0.038

2

  

+

 

g.4323852G>A

SPATA31E1

 

+

 

0.009

0.007

3

 

+

  

g.37453246G>C

NOTCH1

 

+

 

0.023

0.040

4

  

+

 

g.37455302G>A

NOTCH1

0.008

    

9

   

+

g.79813487A>T

ENSECAG00000020135

     

1

+

   

g.25184403G>C

ENSECAG00000021286

     

1

+

   
  1. Significant associations of the high-impact variants with the estimated breeding values of the paternal component for the pregnancy rate per estrus (EBV-PAT) in Hanoverian stallions (n = 216) are indicated by Bonferroni-corrected P-values. For each variant, a plus sign indicates the missing mutant homozygous genotype (GTmissing), high and low heterozygous genotype frequencies (2pqhigh, 2pqlow) and the expected number of mutant homozygous genotypes for stallions E (q2 stallion) are given. The number of breeds where the variants were observed is counted and a grouping (group I-IV) by the minor allele frequency (MAF) is given
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BMC Genomics

ISSN: 1471-2164

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