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Table 2 Genome-wide and chromosome-wide significant SNP and potential candidate genes associated with six morphometric traits from four indigenous breeds in Benin

From: A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

SNP_rs

SNP

CHR

BP_ARS1.2

Alleles

MAF

BETA

P-value

SNP in Gene

Gene Name

A1

A2

PLINK

GCTA

PLINK

GCTA

Height at withers

 rs109126926a

ARS-BFGL-NGS-57889

1

110,160,486

A

G

0.26

2.24

2.16

1.12e-06

1.44e-05

Yes

VEPH1

 rs43347748

ARS-BFGL-NGS-31952

3

81,139,242

C

T

0.10

2.60

1.96

6.44e-06

1.40e-03

–

–

 rs41634361

Hapmap50686-BTA-41836

17

68,037,062

G

A

0.10

2.58

2.40

1.71e-05

1.99e-04

Yes

CCDC117

 rs110369628

ARS-BFGL-NGS-91812

19

20,892,297

T

C

0.02

5.58

4.55

4.82e-05

2.00e-03

Yes

SSH2

 rs109889052

ARS-BFGL-NGS-81151

19

28,301,046

A

G

0.13

2.35

2.08

4.57e-05

7.94e-04

Yes

PIK3R6

 rs109872376

ARS-BFGL-NGS-46597

21

7,674,101

C

G

0.44

1.62

1.54

5.04e-05

2.09e-04

–

–

Sacrum height

 rs111001850

ARS-BFGL-NGS-7310

7

42,545,291

A

G

0.45

1.53

1.50

2.35e-05

1.12e-04

No

LYPD8

 rs110441360

ARS-BFGL-NGS-110086

20

11,381,378

A

G

0.48

−1.51

−1.51

3.86e-05

1.19e-04

No

PIK3R1

Heart girth

 rs110404606

ARS-BFGL-NGS-77689

2

32,163,209

C

T

0.38

2.83

2.55

1.17e-05

9.65e-05

–

–

 rs41579167

BTA-49621-no-rs

2

125,244,296

G

A

0.44

−2.93

−2.75

1.55e-05

5.59e-05

No

PTAFR

EYA3

 rs41624005

Hapmap48676-BTA-18047

19

46,729,603

A

G

0.50

2.72

2.64

1.60e-05

4.29e-05

–

–

 rs41637645

Hapmap39844-BTA-54797

22

48,208,654

C

A

0.16

−3.48

−3.36

4.10e-05

8.96e-05

Yes

PBRM1

Hip width

 rs109866742

ARS-BFGL-NGS-119529

8

103,907,956

T

C

0.02

−3.12

−3.06

2.11e-05

5.89e-05

–

–

 rs41569598

BTA-39611-no-rs

16

56,426,595

C

T

0.43

−0.97

−0.97

2.99e-05

3.88e-05

–

–

 rs42843320

BTB-01732320

16

60,525,984

C

T

0.22

−1.12

−1.15

2.08e-05

1.47e-05

Yes

ABL2

Body length

 rs110694334a

ARS-BFGL-NGS-109828

2

76,610,609

C

T

0.03

−17.96

−11.94

8.19e-07

4.90e-04

yes

CNTNAP5

 rs109186122

ARS-BFGL-NGS-118432

2

78,925,610

C

T

0.25

−7.18

−3.43

9.33e-06

2.48e-02

yes

GYPC

 rs42301516

BTB-01145402

2

113,155,761

G

A

0.43

−5.45

−4.31

1.38e-05

1.37e-04

–

–

 rs135705191

BovineHD0300010335

3

33,048,892

G

A

0.20

−6.85

−3.72

2.49e-05

1.90e-02

yes

SLC16A4

 rs43616983

BTB-00409355

10

12,969,418

G

A

0.20

6.70

6.20

3.41e-05

2.94e-05

yes

MEGF11

 rs42436268

BTB-01308172

17

33,487,976

G

T

0.32

5.45

4.06

4.93e-05

8.18e-04

–

–

 rs41608167

BTA-96370-no-rs

21

3,408,269

T

C

0.02

−18.36

−9.53

3.74e-05

2.29e-02

–

–

 rs41607390a

Hapmap33092-BTA-51753

21

18,775,375

T

C

0.11

−10.39

−7.07

2.03e-07

2.20e-04

–

–

 rs41646754

Hapmap44720-BTA-62525

27

24,546,315

G

C

0.27

−6.28

−4.04

1.91e-05

3.27e-03

–

–

Ear length

 rs109212458

ARS-BFGL-NGS-85383

7

96,266,192

T

C

0.33

0.42

0.38

2.54e-05

1.63e-04

–

–

 rs110608572

ARS-BFGL-NGS-103122

10

12,919,428

A

G

0.03

1.10

1.07

1.86e-05

4.40e-05

Yes

MEGF11

 rs41567897

BTA-100327-no-rs

12

41,375,572

C

G

0.17

−0.59

−0.49

1.08e-05

3.56e-04

–

–

 rs109985119

ARS-BFGL-NGS-44763

20

40,060,386

T

C

0.14

0.56

0.54

1.90e-05

4.23e-05

Yes

ADAMTS12

  1. aGenome-wide significant SNP; the remaining SNP are the chromosome-wide significant SNP
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BMC Genomics

ISSN: 1471-2164

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