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Table 3 Significant SNPs associated with teat number in Canadian Duroc pigs

From: Genome-wide association analyses identify known and novel loci for teat number in Duroc pigs using single-locus and multi-locus models

SSCa

SNP ID

Position (bp)b

MAF

Single-locus GWAS

Multi-locus GWAS

Nearest genee

Distance/bpf

P-value

R2(%)c

Modeld

LOD

R2(%)c

Modeld

1

rs333890665

271,354,424

0.31

1.28E-05

0.8

I

4.86

1.42

V

PRRC2B

within

1

rs321500205

271,382,273

0.45

1.40E-05

0.94

I

4.43–6.09

0.79–1.47

II,III,IV,V

ENSSSCG00000022130

36,815

2

rs81363870

121,140,488

0.49

   

4.02–6.41

4.77–7.26

II,III,IV,V

SEMA6A

453,157

3

rs344649466

5,715,228

0.35

   

3.15–3.51

0.78–1.42

II,III

NPTX2

− 5452

5

rs81384813

66,721,316

0.06

   

3.52

2.54

II

PRMT8

within

5

rs81384838

66,734,388

0.1

   

3.92

1.52

V

PRMT8

within

6

rs324552394

164,807,745

0.24

   

3.58

0.77

V

EFCAB14

within

7

rs80864749

7,655,911

0.36

   

3.24

0.79

III

ELOVL2

within

7

rs330783620

9,154,293

0.15

   

3.18

0.37

IV

PHACTR1

−191,156

7

rs80888936

96,128,654

0.35

2.67E-07

3.78

I

   

ENSSSCG00000033840

122,929

7

rs324614194

96,278,617

0.47

1.11E-14

6.07

I

   

ENSSSCG00000028159

−10,186

7

rs331807204

96,632,217

0.36

1.46E-07

3.9

I

   

NUMB

within

7

rs81265875

96,660,861

0.36

1.38E-07

3.92

I

   

NUMB

within

7

rs329434246

96,694,364

0.36

9.91E-08

3.97

I

   

NUMB

within

7

rs81396029

96,727,497

0.36

1.46E-07

3.9

I

   

NUMB

within

7

rs81295281

96,731,838

0.35

2.25E-07

3.79

I

   

NUMB

within

7

rs81396040

96,743,525

0.36

1.50E-07

3.9

I

   

NUMB

within

7

rs81227580

96,786,714

0.35

2.47E-07

3.79

I

   

NUMB

within

7

rs81396043

96,806,775

0.35

2.49E-07

3.77

I

   

NUMB

6800

7

rs342685919

97,048,514

0.44

1.93E-13

5.84

I

   

ENSSSCG00000035322

−708

7

rs80843834

97,109,772

0.35

1.63E-07

3.76

I

   

ELMSAN1

32,738

7

rs80805264

97,126,583

0.35

1.63E-07

3.76

I

   

ENSSSCG00000002351

−47,593

7

rs327357811

97,347,282

0.33

4.97E-14

5.61

I

   

BBOF1

within

7

rs319296259

97,394,296

0.33

1.76E-13

5.5

I

   

LIN52

within

7

rs346287309

97,427,849

0.33

1.99E-13

5.48

I

   

LIN52

within

7

rs692640845

97,568,284

0.48

7.51E-21

8.68

I

36.46

9.31

V

ABCD4

within

7

rs1113960993

97,575,068

0.48

7.54E-21

8.68

I

   

ABCD4

within

7

rs330032123

97,584,287

0.48

7.54E-21

8.68

I

   

ABCD4

within

7

VRTN_mutation

97,615,880

0.49

6.81E-20

7.8

I

   

VRTN

within

7

rs343248943

97,617,907

0.48

7.54E-21

8.68

I

   

VRTN

within

7

rs80894106

97,652,632

0.48

8.65E-20

8.34

I

   

SYNDIG1L

− 4101

7

rs81238639

97,946,666

0.46

2.28E-09

5.23

I

   

FCF1

within

7

rs80864705

97,954,258

0.46

2.29E-09

5.23

I

   

FCF1

within

7

rs80929215

97,973,860

0.46

2.29E-09

5.23

I

   

YLPM1

− 2277

7

rs80813473

98,066,911

0.47

4.67E-16

7.73

I

   

PROX2

within

7

rs80836267

98,089,286

0.47

5.07E-16

7.71

I

   

DLST

− 1527

7

rs80865802

102,479,725

0.33

5.99E-05

2.98

I

   

ENSSSCG00000021315

within

7

rs338075156

102,513,443

0.33

3.84E-05

3.01

I

   

ENSSSCG00000021315

within

7

rs80975884

102,552,105

0.33

3.84E-05

3.01

I

   

ENSSSCG00000021315

within

7

rs80822795

102,658,822

0.30

3.96E-05

3.02

I

   

ENSSSCG00000021315

within

7

rs80795811

103,109,678

0.19

5.27E-05

2.82

I

   

DIO2

within

7

NA

103,132,435

0.19

5.27E-05

2.82

I

   

DIO2

within

7

rs80847916

103,151,323

0.19

5.27E-05

2.82

I

   

DIO2

within

7

NA

103,164,950

0.19

5.27E-05

2.82

I

   

DIO2

within

8

rs81401285

72,626,638

0.33

   

5.75

0.9

IV

SEPT11

within

8

rs343488415

73,599,016

0.36

   

6.52

2.5

II

FRAS1

within

8

rs81335362

136,866,026

0.16

   

3.28

1.1

V

BMP3

−12,934

10

rs334392548

16,387,485

0.47

   

4.03

0.97

II

SDCCAG8

within

11

rs80803790

6,291,044

0.26

4.86E-06

1.11

I

3.12–5.39

0.51–2.39

II,III,IV,V

MTUS2

within

11

rs80914601

6,324,834

0.27

6.52E-06

0.93

I

   

MTUS2

within

11

rs343377111

15,473,025

0.36

   

3.29

1

II

MRPS31

801

11

rs80930723

70,370,312

0.29

   

3.81–4.21

0.62–1.33

III,IV,V

FGF14

within

12

rs81440983

17,695,233

0.33

   

3.96–4.53

0.84–1.59

II,III

WNT3

within

13

rs335055280

244,235

0.11

   

3.97–5.35

1.60–3.59

II,III

CPNE4

−123,572

13

rs345752157

198,613,309

0.2

   

3.42–3.66

0.86–1.58

II,V

RUNX1

within

14

rs345307243

24,753,992

0.39

   

4.07

0.91

V

PIWIL1

within

14

rs81450840

57,407,462

0.24

   

4.56–6.50

0.77–2.68

II,III,IV,V

ENSSSCG00000010164

−17,318

14

rs80823799

136,408,216

0.18

   

3.31

0.78

III

DOCK1

within

16

rs322985099

6,124,952

0.31

2.53E-05

0.59

I

3.34–4.09

0.48–1.37

II,III,IV,V

MYO10

within

17

rs80843610

8,468,654

0.44

   

3.00–5.39

0.36–1.25

II,III,IV,V

FAT1

within

18

rs321942793

6,398,431

0.26

   

3.94–4.24

1.38–1.99

II,III

GIMAP2

within

18

rs81471144

51,455,200

0.41

   

5.17

1.1

II

HECW1

within

  1. aSus scrofa chromosome b SNP position in Ensembl c Proportion of total phenotypic variation explained by each SNP. Bold text indicates the maximum phenotypic variance explained by the multi-locus model d MLM, mrMLM, FASTmrMLM, FASTmrEMMA and ISIS EM-BLASSO were indicated by I-V, respectively. The bold data represent the model that explained largest phenotypic variance e Underline indicates that the gene was newly identified as a candidate for teat number f The SNP located upstream/downstream of the nearest gene
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BMC Genomics

ISSN: 1471-2164

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