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Table 2 The 59 QTL regions identified by GWAS, the most likely candidate variant, and number of traits affected by the QTL

From: Sequence-based GWAS, network and pathway analyses reveal genes co-associated with milk cheese-making properties and milk composition in Montbéliarde cows

QTL region

Best candidate varianta

Number of traitsd

N

BTA

From (bp)

To (bp)

# variants

#genes

bp

Variant ID

Rank

R2

MAF

Effect

SE

− log10P

Gene

Functional annotation

Trait most strongly affected

CMP

Proteins

Fatty acids

Minerals

1

1

144,389,419

144,398,814

6

1

144,395,375

rs136069703

1

0.97

0.38

29.5

0.951

210.4

SLC37A1

Intron

P

3

1

1

4

2

2

5,718,384

6,567,522

111

5

5,865,070

rs136830094

1

0.91

0.22

− 0.02

0.003

15.6

INPP1

Downstream

Lactose

0

1

0

2

3

2

131,808,301

131,888,417

88

1

131,816,616

rs133677653

1

0.91

0.49

− 0.05

0.003

41.4

ALPL

Intron

κ-CN

1

3

0

1

4

3

7,442,755

8,149,715

56

5

7,935,102

rs383033753

7

0.50

0.14

− 0.65

0.096

10.7

FCGR2B

Intron

CYDM

2

0

1

0

5

3

15,514,034

15,928,379

401

7

15,525,599

rs110073735

1

0.99

0.03

− 2.78

0.410

10.9

EFNA1

Intron

Lactose

1

0

0

3

6

3

34,235,208

34,355,357

35

4

34,327,146

rs210558120

1

0.34

0.43

0.26

0.035

12.9

KIAA1324

Intron

aSC

2

0

0

0

7

4

49,033,707

49,153,995

39

2

49,033,707

rs380575157

1

0.47

0.20

0.02

0.001

30.7

CBLL1

Upstream

pH0_PCC

2

3

0

2

8

4

75,743,094

79,803,738

59

5

77,825,429

rs385069094

1

0.57

0.01

− 2.34

0.360

10.1

GCK

Intron

Mg

0

1

0

3

9

4

92,588,016

92,966,245

227

7

92,624,543

rs379514460

1

0.34

0.03

− 29.0

4.226

11.2

FSCN3

Upstream

Ca

0

0

0

1

10

5

29,947,476

31,423,430

315

25

29,947,476

rs442522314

2

0.63

0.09

− 2.26

0.383

8.4

COX14

Downstream

Lactose

0

0

0

1

11

5

93,892,583

93,945,738

9

1

93,943,700

rs210744452

1

0.77

0.05

0.11

0.010

27.7

MGST1

Intron

FC

2

0

7

0

12

5

117,126,900

119,221,867

51

3

117,972,265

rs525880746

1

0.79

0.04

42.4

2.186

83.0

GRAMD4

Upstream

Ca

7

4

1

6

13

6

37,857,989

38,326,250

268

8

38,326,250

rs382477515

1

0.37

0.42

− 0.10

0.017

9.5

IBSP

Upstream

β-CN

0

1

0

0

14

6

46,555,489

47,082,793

89

3

46,876,802

rs110408618

1

1.00

0.17

27.8

1.189

120.5

SEL1L3

Intron

K

4

5

1

4

15

6

87,125,482

87,961,577

143

7

87,392,899

rs382350292

3

0.53

0.23

0.03

0.002

76.4

CSN3

Downstream

K10/RSC

8

8

0

1

16

6

108,967,622

109,145,154

91

5

109,026,822

rs208213463

1

0.93

0.47

− 8.42

0.904

19.9

GAK

Intron

Ca

2

2

0

2

17

7

958,741

1,146,962

359

4

975,515

rs383246531

1

0.93

0.37

− 1.56

0.180

17.4

47695b

Intron

Lactose

0

0

0

2

18

7

41,576,519

46,646,915

399

23

46,452,656

rs209828204

6

0.87

0.07

1.36

0.127

26.0

FSTL4

Downstream

aPCC

2

2

0

1

19

9

102,731,669

103,130,410

207

3

102,885,120

rs134445867

15

0.90

0.03

− 0.14

0.023

9.3

MPC1

Intron

C4_C10

0

0

1

0

20

10

1,984,741

2,326,212

86

1

2,096,282

rs385793060

67

0.99

0.35

− 2.04

0.380

7.1

47622b

Upstream

Na

0

0

0

1

21

10

48,359,318

50,266,445

213

1

49,459,919

rs109896326

1

1.00

0.14

0.30

0.046

9.8

RORA

Intron

UNSAT

0

0

4

0

22

10

99,714,774

99,843,583

20

0

99,714,774

rs440530756

1

0.22

0.02

− 0.18

0.028

9.8

Intergenic

PUNSAT

0

0

2

0

23

11

9,023,594

9,684,851

11

3

9,684,851

rs384459785

8

0.62

0.07

− 2.82

0.385

12.6

POLE4

Intron

CYFAT-PROT

3

0

3

0

24

11

14,152,677

15,493,112

132

6

14,284,886

rs384594145

48

0.90

0.10

− 0.01

0.001

18.7

XDH

Upstream

pH0_PCC

1

0

0

1

25

11

86,907,041

86,916,295

9

1

86,912,990

rs481567394

1

0.21

0.05

0.02

0.003

16.7

ATP6V1C2

Intron

pH0_PCC

1

0

0

0

26

11

103,273,963

103,322,890

214

4

103,301,982

rs109907194

48

0.89

0.46

− 1.09

0.017

559.7

PAEP

Intron

ΣWP

8

7

2

3

27

12

68,616,690

77,578,414

337

7

70,162,028

rs721489054

22

0.83

0.17

0.22

0.019

29.0

ABCC4

Intron

C14:0

0

0

7

2

28

13

20,094,707

22,437,171

291

4

21,053,894

rs378591536

7

0.34

0.07

− 0.24

0.034

12.1

23216b

Intron

C14:0

0

0

1

0

29

13

45,394,264

48,611,254

75

4

46,734,011

rs379821485

18

0.76

0.15

− 0.01

0.001

10.6

RF0026

Downstream

pH0_PCC

1

0

1

0

30

13

52,289,279

55,114,121

80

9

54,938,610

rs110422533

2

1.00

0.39

− 6.60

1.007

10.3

GID8

Synonymous

K

0

0

2

1

31

13

64,648,620

64,870,118

19

3

64,812,464

rs43717459

1

0.33

0.10

− 0.24

0.027

18.9

ACSS2

Intron

C4–C10

0

0

1

0

32

13

79,225,285

79,326,265

6

1

79,326,265

rs109862148

3

0.38

0.07

− 0.04

0.007

8.9

FAM65C

Downstream

αs2-CN

0

1

0

0

33

14

1,622,956

1,881,116

27

9

1,629,753

rs109035586

1

0.36

0.33

0.17

0.007

122.7

GPT

Upstream

FC

6

6

10

4

34

15

39,854,757

40,283,508

140

2

39,885,845

rs134953698

2

0.79

0.18

− 0.04

0.005

10.4

ARNTL

Intron

PUNSAT

0

0

1

0

35

15

52,993,384

54,612,060

341

10

53,943,342

rs381948106

1

0.47

0.04

17.5

2.747

9.7

RAB6A

Intron

P

0

0

2

2

36

16

1,607,369

3,050,452

10

0

1,609,129

rs42450079

1

0.54

0.28

− 0.04

0.005

17.0

Intergenic

κ-CN

2

6

0

0

37

16

60,539,357

63,891,341

178

3

60,646,127

rs137615589

72

0.75

0.14

0.02

0.004

9.8

38238b

Upstream

aSC

2

1

0

0

38

16

67,700,538

67,811,269

167

2

67,758,163

rs42465711

1

1.00

0.4

0.31

0.044

11.9

SWT1

Intron

CYDM

2

1

2

1

39

16

70,170,086

71,493,899

59

1

71,432,479

rs109766366

5

0.79

0.43

− 0.23

0.032

12.3

PROX1

Intron

UNSAT

0

0

4

2

40

17

29,348,215

30,211,790

203

9

29,938,428

rs207509104

21

0.55

0.36

0.10

0.015

10.3

LARP1B

Synonymous

C4–C10

0

0

1

0

41

17

52,753,338

53,240,467

283

6

53,072,959

rs448501071

5

1.00

0.06

− 0.32

0.019

62.4

BRI3BP

Intron

C4–C10

2

3

2

1

42

18

10,566,605

11,091,131

68

5

11,002,789

rs41867427

2

0.61

0.06

14.3

2.071

11.3

CRISPLD2

Intron

aSC

2

0

0

1

43

19

51,304,834

51,538,272

67

2

51,383,847

rs136067046

1

0.83

0.32

0.20

0.013

49.4

FASN

Upstream

C14:0

0

0

9

0

44

19

55,229,384

57,240,571

267

10

57,151,350

rs42848485

1

0.63

0.46

9.07

1.079

16.4

FADS6

Intron

Ca

2

1

1

1

45

19

60,407,923

62,177,206

142

0

61,135,270

rs41923848

1

0.91

0.13

− 2.28

0.210

26.6

Intergenic

Lactose

0

3

0

3

46

20

58,245,970

58,457,768

87

1

58,446,058

rs137085630

22

0.99

0.06

− 1.01

0.036

176.5

ANKH

Intron

Citrate

5

4

2

5

47

21

40,120,343

44,138,058

63

2

41,638,428

rs137153434

25

0.21

0.12

0.07

0.009

12.7

G2E3

Upstream

PC

3

1

0

1

48

22

32,877,755

33,466,544

46

2

32,877,755

rs208141216

10

0.30

0.08

0.08

0.007

25.7

FAM19A4

Intron

PC

8

1

1

2

49

22

55,186,094

55,273,619

72

1

55,254,221

rs43597796

1

0.93

0.49

0.00

0.001

12.6

ATP2B2

Intron

pH0_PCC

1

1

0

0

50

22

61,257,725

61,312,492

18

1

61,284,069

rs109001472

1

1.00

0.47

− 0.09

0.008

28.3

KLF15

Intron

C4–C10

0

0

2

0

51

24

50,420,365

50,550,020

114

2

50,465,348

rs383068825

4

0.53

0.34

− 10.7

1.282

16.0

SKA1

Downstream

K

1

1

0

2

52

24

58,744,952

58,825,217

23

3

58,817,202

rs208779762

1

0.93

0.43

− 6.57

0.807

15.4

LMAN1

Upstream

P

1

1

0

1

53

25

2,994,081

3,261,509

28

3

3,241,838

rs137696417

16

0.61

0.18

− 0.03

0.007

6.5

ADCY9

Downstream

κ-CN

0

1

0

0

54

25

25,642,563

29,605,418

82

11

26,498,356

rs137150057

1

1.00

0.34

− 0.11

0.020

11.3

FAM57B

5′UTR

C18:0

1

1

6

0

55

26

20,727,700

21,427,109

61

4

21149234

rs136334180

11

1.00

0.31

0.39

0.035

27.6

SCD

Upstream

UNSAT

0

0

11

0

56

26

32,773,808

33,925,908

95

2

33,233,277

rs385554497

36

0.27

0.02

1.55

0.270

8.1

ACSL5

intron

aPCC

1

0

0

0

57

27

36,165,492

36,235,730

11

1

36,212,352

rs208675276

1

0.54

0.41

0.65

0.040

60.4

GPAT4c

5′ UTR

C16:0

3

0

7

1

58

28

6,008,464

7,038,810

141

3

6,027,037

rs382911338

1

0.37

0.18

− 0.01

0.001

17.1

PCNX2

Intron

pH0_PCC

1

2

0

1

59

29

9,253,006

9,622,389

145

3

9,343,362

rs133715120

6

0.61

0.33

− 2.76

0.264

24.9

EED

Intron

Lactose

0

3

1

4

  1. aWhen a gene was present in the confidence interval of the QTL, the best candidate variant was the genic variant with the most significant effects (intergenic variants were discarded)
  2. b47695, 47622, 23216, and 38238 for ENSBTAG00000047695, ENSBTAG00000047622, ENSBTAG00000023216, and ENSBTAG00000038238, respectively
  3. cAlso named AGPAT6
  4. dNumber of milk cheese-making (CMP), protein, fatty acid, and mineral composition traits with significant effects