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Table 3 Identity, position, and effects of significantly associated dominance SNPs obtained by single SNP regression mixed model for birth weight (BWT), weaning weight (WWT), pre-weaning daily gain (PDG), yearling weight (YWT) and marbling score (MBS) in beef cattle

From: Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle

Traits

Groups

SNP reference

BTA

Position

MAF

p value

FDR (%)

Allele substitution effects

Dominance effects

Genes

Region

BWT (kg)

C

rs110704582

1

113,215,525

0.327

4.60e−07

5

0.404

− 0.942

U6atac

Intergenic

C

rs41596755

6

55,697,300

0.244

3.91e−06

10

0.552

1.012

–

Intergenic

WWT (kg)

P

rs42779004

21

36,186,103

0.196

2.74e−07

5

− 4.016

6.994

bta-mir-2888-1

Intergenic

 

A

rs29027109

3

98,222,548

0.387

2.64e−07

5

− 0.361

2.610

AGBL4

Intron

PDG (kg/d)

P

rs42779004

21

36,186,103

0.196

1.89e−06

10

− 0.019

0.037

bta-mir-2888-1

Intergenic

A

rs29027109

3

98,222,548

0.387

2.29e−06

10

− 0.001

0.016

AGBL4

Intron

YWT (kg)

C

rs109808526

4

113,614,764

0.318

1.18e−06

10

− 1.562

6.316

REPIN1

Intergenic

MBS

A

rs110361335

4

17,230,513

0.182

6.47e−07

5

8.317

13.88

ICA1

Intron

A

rs110564527

4

17,657,399

0.207

1.20e−07

5

− 8.023

15.37

NXPH1

Intergenic

  1. P = purebred sample included individuals with > 80% of Angus, Hereford and Charolais (n = 1467); C = crossbred sample included Kinsella composite, Beefbooster TX composite (www.beefbooster.com) and two and more way crosses involving Angus, Hereford, Charolais, Gelbvieh, Simmental, Limousin, and Piedmontese breeds (n = 5327); A = combined data of all individuals in the study (n = 6794)