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Table 7 GWAS validation results for production traits in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) cows

From: Confirmed effects of candidate variants for milk production, udder health, and udder morphology in dairy cattle

QTL IDa

BTA

Breed

Traits (# QTLb)

Candidate variantsc

50K SNPs

Variant with the most significant effect

Total#

# with -log10(P) > 6

# in TOP10

Best rank

Total#

# with -log10(P) > 6

# in TOP10

Best rank

Position (pb)

ID

-log10(P)

Functional annotation

1

3

MON

PC(1)

8

0

4

1

18

0

6

2

14,889,296

rs110992770

2.7

KHCD4 upstream

2

3

HOL

PC(2)

16

3

4

1

31

3

6

3

15,592,645

rs134511693

66.6

EFNA4 upstream/ADAM15 downstream

3

3

NOR

PC(1)

9

4

6

1

15

2

4

3

15,558,071

rs135107424

16.0

Intergenic

4

4

NOR

PC(1)

1

0

0

15

23

3

10

1

78,114,069

rs42683912

10.6

COA1 intron

5

5

MON

FC(1)

2

0

2

5

22

0

8

1

86,753,605

rs109647158

1.7

SOX5 intron

6

5

HOL

PY(1)

18

0

8

1

9

0

2

4

88,830,128

rs136903701

5.5

ABCC9 intron/downstream

7

5

MON

FC(3)

37

17

10

1

51

3

0

16

93,945,738

rs211210569

40.8

MGST1 intron

8

5

HOL

FC(6)

51

33

10

1

95

16

0

30

93,945,991

rs208248675

120.3

MGST1 intron

8

5

HOL

FY(1)

31

26

10

1

3

0

0

29

93,945,738

rs211210569

25.2

MGST1 intron

9

5

NOR

FC(4)

40

25

10

1

57

4

0

24

93,945,738

rs211210569

26.8

MGST1 intron

10

5

NOR

MY(1)

16

0

8

1

4

0

2

2

112,398,982

rs211569025

2.1

Intergenic

11

5

MON

PC(3)

22

9

7

1

75

10

3

2

117,972,265

rs525880746

68.6

GRAMD4 upstream

12

5

HOL

PC(1)

5

1

1

1

32

1

9

2

118,244,695

rs456403270

23.5

TBC1D22A missense

13

6

HOL

FC(1)

8

0

3

1

21

0

7

3

37,723,413

rs136548039

2.9

HERC5 intron

13

6

HOL

PC(1)

6

0

3

3

13

0

7

1

38,063,313

rs41622323

4.4

PKD2 intron

14

6

HOL

PC(7)

174

89

10

1

104

20

0

27

87,199,843

rs383909572

56.0

HSTN splice acceptor

14

6

HOL

PY(1)

87

35

8

1

18

2

2

5

87,181,619

rs43703011

14.6

CSN2 missense

15

6

NOR

PC(8)

192

99

10

1

158

23

0

33

87,296,809

rs134776019

25.3

Intergenic

16

6

MON

PC(10)

190

92

9

1

164

29

1

2

87,296,809

rs134776019

54.4

Intergenic

17

6

MON

PC(1)

10

0

2

4

30

0

8

1

92,623,916

rs41256838

2.1

CXCL10 5′UTR/ART3 intron

18

6

NOR

PC(1)

8

3

6

1

23

3

4

2

92,561,862

rs133076983

6.8

SDAD1 missense

19

11

HOL

FC(1)

31

30

10

1

4

1

0

28

103,300,548

rs109982707

26.3

PAEP upstream

20

14

NOR

FC(5)

73

44

13

1

188

15

0

14

1,891,657

rs109136389

137.6

MROH1 intron

20

14

NOR

FY(1)

39

24

20

1

3

3

1

2

1,808,145

rs135258919

10.2

HSF1 missense/DGAT1 downstream

20

14

NOR

PC(1)

43

41

14

1

7

4

1

2

1,881,116

rs132649038

26.4

MROH1 intron/bta-mir-1839 downstream

21

14

MON

FC(7)

61

22

9

1

224

27

1

10

1,795,176

rs379230475

129.4

DGAT1 5′UTR/SCRT1 downstream

21

14

MON

MY(1)

17

15

10

1

13

5

0

12

1,795,176

rs379230475

18.0

DGAT1 5′UTR/SCRT1 downstream

21

14

MON

FY(1)

17

10

10

1

13

0

0

11

1,639,005

rs384162250

8.8

Intergenic

22

14

HOL

FC(5)

90

52

37

1

206

33

2

1

1,802,265

rs109234250

>300

DGAT1 missense

22

14

HOL

MY(5)

72

48

11

2

139

24

1

1

1,801,116

rs109421300

108.1

DGAT1 intron/HSF1 downstream

22

14

HOL

FY(6)

90

50

10

1

206

26

0

19

1,739,885

rs110825388

93.7

CPSF1 intron/ADCK5 downstream

22

14

HOL

PY(2)

53

45

11

2

30

8

1

1

1,801,116

rs109421300

30.3

DGAT1 intron

22

14

HOL

PC(3)

62

48

13

1

64

18

0

20

1,724,688

rs135458711

141.9

SLC39A4 downstream/CPSF1 upstream

23

14

MON

FC(1)

0

0

0

0

10

0

10

1

12,672,880

rs42381926

1.6

Intergenic

24

14

HOL

FC(3)

1

1

1

3

27

10

9

1

67,443,766

rs109007040

11.9

VPS13B intron

24

14

HOL

MY(3)

4

2

2

4

51

4

8

1

67,443,766

rs109007040

6.2

VPS13B intron

24

14

HOL

PC(5)

5

3

2

4

90

23

8

1

67,443,766

rs109007040

31.0

VPS13B intron

25

15

HOL

PC(1)

0

0

0

0

27

0

10

1

27,905,645

rs110144962

2.5

APOA4 downstream

26

16

MON

PC(1)

1

1

1

1

13

0

9

2

60,692,234

rs135698521

7.9

Intergenic

27

19

HOL

FC(1)

11

9

9

1

3

1

1

4

51,319,797

rs41921161

16.6

CCDC57 missense

27

19

HOL

FY(1)

11

0

9

1

3

0

1

4

51,319,797

rs41921161

5.9

CCDC57 missense

28

20

HOL

FY(1)

5

0

3

4

7

0

7

1

7,661,649

rs110231369

0.5

ARHGEF28 intron

28

20

HOL

PY(1)

4

0

4

3

5

0

5

1

7,661,649

rs110231369

0.8

ARHGEF28 intron

29

20

HOL

PC(1)

1

1

1

1

11

2

9

2

30,005,528

rs43140727

11.3

Intergenic

30

20

HOL

PC(3)

103

92

10

1

48

12

0

50

31,909,478

rs385640152

102.4

GHR missense

30

20

HOL

MY(1)

80

37

14

1

23

0

0

41

31,303,953

rs474736745

9.9

PAIP1 intron

30

20

HOL

FC(3)

103

82

10

1

48

6

0

46

31,909,478

rs385640152

54.5

GHR missense

31

22

MON

PC(1)

3

0

3

3

4

1

4

1

32,827,786

rs41642478

1.0

TAFA4 intron

32

27

MON

FC(1)

8

4

6

1

7

2

4

5

36,209,319

rs211250281

20.4

GPAT4 upstream

33

27

HOL

FC(1)

5

4

5

1

6

4

5

5

36,212,352

rs208675276

33.3

GPAT4 5′ UTR

34

27

NOR

FC(1)

8

4

7

1

8

2

4

5

36,211,258

rs209479876

14.7

GPAT4 upstream

35

29

HOL

PC(1)

4

2

3

1

15

1

7

2

9,608,833

rs378017490

10.0

PICALM upstream

36.

29

HOL

PC(2)

50

5

5

1

56

4

5

4

41,843,734

rs208817293

15.9

WDR74 intron/U2 downstream

  1. #: number of
  2. aID number associated with a group of QTL linked with milk production traits that had overlapping confidence intervals or less than 1 Mbp distance between the bounds of the confidence intervals
  3. bIndividual QTL; milk yield (MY), fat content (FC), protein content (PC), fat yield (FY), protein yield (PY)
  4. cCandidate variants selected from sequence-based GWAS results