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Table 11 Ten SNPs significantly associated with AGE (difference, in months, between each pig’s birth date and January 2006) with the largest absolute values for SNP effects within the Duroc, Landrace, Yorkshire, and crossbred populations

From: Analysis of polygenic selection in purebred and crossbred pig genomes using generation proxy selection mapping

Subset

Populations

SNP identifiera

MAF

SNP effect

SE

Q-value

Number of subsets in which SNP was significant

1

Duroc

3420

0.24

13.32

0.310

1.49E−102

3

41,017

0.02

8.21

0.648

3.54E−33

1

30,819

0.07

7.71

0.368

2.05E−93

2

35,689

0.09

6.49

0.390

2.34E−58

3

39,502

0.47

6.19

0.353

1.24E−64

3

18,513

0.02

5.16

0.643

2.28E−12

1

30,855

0.13

4.87

1.025

1.56E−03

1

49,794

0.38

4.79

0.340

1.56E−41

3

31,005

0.11

4.66

0.880

1.31E−04

1

6055

0.08

4.60

0.370

5.40E−32

3

2

Landrace

39,502

0.30

6.64

0.302

1.76E−102

3

14,465

0.02

4.40

0.518

9.00E−14

3

1063

0.46

3.95

0.207

3.69E−77

1

22,747

0.31

3.81

0.333

2.43E−26

1

10,745

0.42

3.52

0.206

2.66E−61

2

38,925

0.04

3.51

0.840

1.55E−02

1

6055

0.18

3.08

0.238

2.03E−34

3

485

0.23

3.08

0.325

1.71E−17

2

39,264

0.28

3.03

0.418

9.58E−10

1

8174

0.29

3.00

0.456

8.35E−08

2

3

Yorkshire

45,804

0.02

6.00

0.664

1.14E−15

1

39,502

0.36

4.03

0.316

4.80E−33

3

19,756

0.17

3.40

0.486

7.20E−09

1

35,689

0.28

3.28

0.284

1.24E−26

3

9883

0.39

3.05

0.385

1.20E−11

2

8174

0.14

3.03

0.437

1.02E−08

2

41,553

0.43

2.96

0.188

5.05E−51

1

30,156

0.04

2.87

0.790

9.16E−02

1

34,751

0.05

2.52

0.461

5.84E−05

3

34,530

0.18

2.38

0.277

6.05E−14

2

4

Crossbred

30,819

0.07

14.39

0.372

1.81E−102

2

14,465

0.02

5.10

0.536

9.90E−18

3

3834

0.04

4.01

0.344

1.58E−27

2

36,398

0.18

4.00

0.288

1.25E−39

2

31,018

0.48

3.52

0.281

7.71E−32

1

6187

0.40

3.06

0.241

1.00E−32

3

3420

0.43

2.99

0.271

2.72E−24

3

43,184

0.08

2.77

0.282

7.68E−19

4

33,882

0.07

2.09

0.290

1.63E−09

3

4012

0.13

2.00

0.258

4.15E−11

1

  1. MAF minor allele frequency, SE standard error
  2. aAnonymous SNP identifiers were used to protect the intellectual property of The Maschhoff’s, LLC
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Genetics Selection Evolution

ISSN: 1297-9686