Table 2

SNP marker associations and estimated effects for ADFI and ADG in the discovery population of crossbred steers.

Average Daily Feed Intake (ADFI)

Average Daily Gain (ADG)


Marker1

Gene2

Position3

IUB

# Genotypes4

MAF

Effect5

P-value

Correction6

Effect

P-value

Correction


ARS-BFGL-NGS-77584

37855236

R

1182

G = 0.10

-0.026

0.8

NS

-0.0078

0.7

NS

After2Run10KSet7323

37856744

Y

1075

T = 0.30

-0.14

0.01

NS

-0.029

0.01

NS

Hapmap31601-BTC-034240

37859827

R

1076

G = 0.28

-0.15

0.005

NS

-0.033

0.004

NS

Hapmap28705-BTC-034230

37862818

S

1090

G = 0.31

-0.14

0.010

NS

-0.033

0.003

NS

Hapmap25169-BTC-034210

37870369

R

1186

A = 0.30

-0.15

0.006

NS

-0.033

0.003

NS

Hapmap30444-BTC-052947

37875093

Y

1164

C = 0.49

0.16

0.004

NS

0.036

0.002

NS

After2Run10KSet5598

37875791

Y

1186

C = 0.30

-0.14

0.01

NS

-0.032

0.004

NS

Hapmap32743-BTC-052998

37879284

R

1011

A = 0.23

-0.073

0.2

NS

-0.024

0.04

NS

Hapmap23977-BTC-053017

37880952

M

1176

A = 0.30

-0.15

0.006

NS

-0.032

0.005

NS

79140_312

LAP3

37964162

INDEL

1165

DEL = 0.09

0.11

0.2

NS

-0.013

0.5

NS

Hapmap56977-ss46527055

LAP3

37967630

R

1192

A = 0.13

-0.051

0.5

NS

-0.013

0.4

NS

79152_265

LAP3

37977863

Y

1181

C = 0.33

-0.020

0.7

NS

-0.021

0.05

NS

79154_194

LAP3

37979109

Y

1078

T = 0.38

-0.0072

0.9

NS

-0.021

0.06

NS

79154_347

LAP3

37979262

S

1098

C = 0.34

-0.022

0.7

NS

-0.021

0.04

NS

79158_103

LAP3

37984197

S

1193

G = 0.34

0.026

0.6

NS

0.021

0.05

NS

79158_104

LAP3

37984198

R

1190

G = 0.33

-0.021

0.7

NS

-0.020

0.07

NS

79160_105

LAP3

37985986

Y

1127

T = 0.34

-0.0086

0.9

NS

-0.019

0.08

NS

79162_241

LAP3

37986804

K

1124

T = 0.37

-0.0064

0.9

NS

-0.22

0.05

NS

79162_246

LAP3

37986809

Y

1197

C = 0.34

-0.020

0.7

NS

-0.21

0.04

NS

ARS-BFGL-NGS-44699

38011603

S

1183

C = 0.10

-0.085

0.3

NS

-0.021

0.2

NS

BTA-100891

38076964

Y

1063

T = 0.26

-0.083

0.1

NS

-0.028

0.008

NS

83704_2347

NCAPG

38157198

R

1085

A = 0.42

0.18

0.0006

0.03

0.046

2.E-05

0.0009

83704_366

NCAPG

38157330

R

1187

G = 0.12

-0.11

0.2

NS

-0.013

0.4

NS

83708_361

NCAPG

38158932

Y

1092

C = 0.41

0.17

0.001

0.05

0.045

4.E-05

0.002

83712_1687

NCAPG

38163729

R

1004

G = 0.47

-0.16

0.003

NS

-0.045

9.E-05

0.004

83714_2247

NCAPG

38164403

K

1132

G = 0.34

0.21

8.E-05

0.004

0.059

1.E-07

5.E-06

83724_658

NCAPG

38180790

Y

1100

C = 0.41

0.17

0.001

0.05

0.045

5.E-05

0.002

83730_778

NCAPG

38195339

M

1022

A = 0.42

0.17

0.003

NS

0.058

1.E-06

0.00005

83732_316

NCAPG

38195743

R

1050

G = 0.42

0.14

0.008

NS

0.044

1.E-04

0.005

Hapmap24122-BTC-041153

38217816

K

1193

G = 0.35

0.22

1.E-05

0.0005

0.059

2.E-08

9.E-07

Hapmap24041-BTC-041151

38220879

K

1192

T = 0.35

0.22

1.E-05

0.0005

0.059

2.E-08

9.E-07

Hapmap31609-BTC-041148

38223329

R

1192

A = 0.38

0.17

0.0005

0.02

0.045

1.E-05

0.0005

Hapmap28154-BTC-0411348

LCORL

38228679

R

935

C = 0.38

0.18

0.0003

0.01

0.045

2.E-05

0.0009

Hapmap27082-BTC-041131

LCORL

38233962

R

1121

G = 0.37

0.18

0.0002

0.009

0.047

4.E-06

0.0002

Hapmap26855-BTC-041123

LCORL

38239191

R

1075

G = 0.33

0.21

8.E-05

0.004

0.058

1.E-07

5.E-06

Hapmap23341-BTC-041113

LCORL

38250098

K

1161

T = 0.36

0.21

4.E-05

0.002

0.056

1.E-07

5.E-06

81441_243

LCORL

38255270

S

822

G = 0.28

-0.24

5.E-06

0.0002

-0.058

2.E-07

9E-06

81435_188

LCORL

38284737

Y

892

C = 0.38

0.17

0.0004

0.02

0.042

3.E-05

0.001

Hapmap28589-BTC-0410459

LCORL

38300298

S

1190

G = 0.33

0.22

2.E-05

0.0009

0.061

1.E-08

5.E-07

Hapmap33629-BTC-041038

LCORL

38313142

Y

999

T = 0.30

0.22

2.E-05

0.0009

0.059

5.E-08

2.E-06

Hapmap28835-BTC-041022

LCORL

38326993

S

1061

G = 0.18

-0.12

0.07

NS

-0.027

0.04

NS

81419_461

LCORL

38342145

M

1058

C = 0.05

-0.17

0.1

NS

-0.046

0.04

NS

Hapmap33694-BTC-041005

LCORL

38342183

R

1190

G = 0.16

-0.10

0.1

NS

-0.038

0.005

NS

81405_2829

LCORL

38376731

M

1196

A = 0.33

0.22

2.E-05

0.0009

0.061

1.E-08

5.E-07

Hapmap33650-BTC-073421

38409471

Y

1041

C = 0.40

-0.14

0.004

NS

-0.036

0.0003

0.01

Hapmap31943-BTC-050642

38427989

Y

1181

C = 0.08

-0.11

0.2

NS

-0.039

0.02

NS

BTB-00249053

38481012

Y

1183

T = 0.24

-0.12

0.03

NS

-0.029

0.01

NS


1 Name of publicly available markers from the following references: Van Tassell CP et al. [26], Bovine HapMap Consortium et al. [27], and Bovine Genome Sequencing and Analysis Consortium et al. [28]

2 SNP located within a gene locus are presented in this column. The gene loci for LAP3, NCAPG, and LCORL are: 37,961,725 - 37,987,164 bp, 38,153,047-38,199,153 bp, and 38,227,955-38,378,385 bp on the Btau 4.0 genome assembly.

3 Position based on the Btau 4.0 Bovine Genome Assembly.

4 Number of genotypic calls used for statistical analysis.

5 ADFI and ADG effects are displayed as kg/d. Effects are presented for the minor allele.

6 Correction for multiple testing performed by multiplying the P-values by the number of markers tested (n = 47). NS = not significant, P-value > 0.05.

7 Markers evaluated in Setoguchi et al. [8] and Eberlein et al. [11].

8 Marker evaluated in Charolais and German Holstein population in Eberlein et al. [11].

9 Markers in bold font, Hapmap28589-BTC-041045 and 81405_282, were significantly associated with ADG in the validation population of animals (P = 0.04 and 0.03, respectively).

Lindholm-Perry et al. BMC Genetics 2011 12:103   doi:10.1186/1471-2156-12-103

Open Data