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Table 5 QTL detected for milk production traits in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) bulls

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

QTL IDa

BTA

Breed

Traits (# QTLb)

CI of the TOP-CIc

Variant with the most significant effect

CI of the EXT-CIf

Bounds (Mbp)

# Genes

Position (bp)

Variant ID

Functional annotation

MAF

–log10(P)

be

sd

Bounds (Mbp)

# Genes

1

3

MON

PC(1)

13.8–15.0

10

14,278,689

rs443751026

GPATCH4 upstream

0.02

9.2

− 0.667

0.108

13.8–15.0

10

2

3

HOL

PC(2)

15.3–15.9

16

15,540,709

rs207616487

Intergenic

0.03

23.3

− 0.461

0.046

13.6–15.9

19

3

3

NOR

PC(1)

14.7–15.6

6

15,558,071

rs135107424

Intergenic

0.31

12.7

− 0.278

0.038

14.7–15.6

6

4

4

NOR

PC(1)

77.8–79.2

8

78,878,576

rs209194403

Intergenic

0.12

8.6

0.307

0.052

77.8–79.2

8

5

5

MON

FC(1)

85.0–86.8

1

85,867,738

rs378424416

48719* intron

0.03

9.2

− 0.53

0.086

85.0–86.8

1

6

5

HOL

PY(1)

88.6–89.2

5

89,037,941

rs441042365

GYS2 intron

0.05

8.3

− 0.273

0.047

88.6-89.2

5

7

5

MON

FC(3)

93.7–94.0

2

93,912,041

rs208512412

Intergenic

0.13

10.7

− 0.318

0.048

89.7–94.0

5

8

5

HOL

FC(6)

93.8–94.0

2

93,944,234

rs210886822

MGST1 intron

0.44

26.4

0.242

0.022

90.8–98.2

13

8

5

HOL

FY(1)

93.9–94.1

2

93,954,751

rs209288972

MGST1 upstream

0.214

12.3

0.1883

0.026

93.9–94.1

2

9

5

NOR

FC(4)

93.9–94.2

1

94,159,666

rs384934968

Intergenic

0.16

13.6

− 0.335

0.044

89.1–94.2

7

10

5

NOR

MY(1)

112.2–112.5

3

112,281,738

rs110231840

MRTFA intron

0.07

8.3

− 0.389

0.066

112.2–112.5

3

11

5

MON

PC(3)

117.1–118.6

8

118,007,875

rs474313622

GRAMD4 intron

0.04

18.9

− 0.683

0.075

117.1–121.1

15

12

5

HOL

PC(1)

117.8–119.1

3

118,283,121

rs483019568

TBC1D22A intron

0.2

11.3

− 0.167

0.024

117.8–119.1

3

13

6

HOL

FC(1)

37.5–38.5

6

37,742,024

rs458142329

HERC6 intron

0.01

9.7

− 0.442

0.069

37.5–38.5

6

13

6

HOL

PC(1)

37.5–38.1

5

37,742,024

rs458142329

HERC6 intron

0.012

24.3

− 0.701

0.068

37.5–38.1

5

14

6

HOL

PC(7)

86.0–87.6

4

87,001,138

rs109613975

38214d intron

0.11

24.1

0.448

0.043

81.7–90.3

18

14

6

HOL

PY(1)

86.9–88

7

87,174,212

rs110217592

Intergenic

0.313

9.6

− 0.156

0.025

86.9–88

7

15

6

NOR

PC(8)

86.5–87.6

4

87,172,459

rs109761275

Intergenic

0.5

22.1

− 0.399

0.041

78.9–91.0

15

16

6

MON

PC(10)

86.6–88.4

8

87,592,824

rs386045066

Intergenic

0.29

23.1

0.411

0.041

78.3–91.2

17

17

6

MON

PC(1)

92.4–94.0

4

93,148,097

rs132964769

SHROOM3 intron

0.43

8.9

0.224

0.037

92.4–94

4

18

6

NOR

PC(1)

92.4–93.5

4

93,231,665

rs43475602

SHROOM3 intron

0.25

9.5

0.32

0.051

92.4–93.5

4

19

11

HOL

FC(1)

103.2–103.4

3

103,294,772

rs207607053

Intergenic

0.48

10.2

0.13

0.02

103.2–103.4

3

20

14

NOR

FC(5)

1.5–2.0

19

1,800,399

rs208317364

DGAT1 intron/HSF1 downstream

0.09

89.0

1.04

0.052

1.5–9.3

33

20

14

NOR

FY(1)

1.7–2

19

1,810,124

rs133931291

HSF1 intron

0.09

14.3

0.4301

0.055

1.7–2

19

20

14

NOR

PC(1)

1.5–2

19

1,800,399

rs208317364

DGAT1 intron/HSF1 downstream

0.094

14.5

0.417

0.053

1.5–2

19

21

14

MON

FC(7)

1.4–2.0

23

1,881,116

rs132649038

MROH1 intron/bta-mir-1839 downstream

0.02

62.4

1.935

0.115

1.4–10.5

45

21

14

MON

MY(1)

1.4–2.3

24

2,261,103

rs517360248

ZNF623 downstream

0.169

9.9

− 0.239

0.037

1.4–2.3

24

21

14

MON

FY(1)

1.4–2.3

24

2,261,103

rs517360248

ZNF623 downstream

0.169

9.9

− 0.239

0.037

1.4–2.3

24

22

14

HOL

FC(5)

1.8–3.0

19

1,881,400

rs210517654

MROH1 intron/bta-mir-1839 downstream

0.2

295.1

0.916

0.022

1.5–9.7

55

22

14

HOL

MY(5)

1.5–2.1

29

1,801,116

rs109421300

DGAT1 intron/HSF1 downstream

0.203

100.8

− 0.49

0.023

1.5–7.1

29

22

14

HOL

FY(6)

1.5–2.2

29

1,801,116

rs109421300

DGAT1 intron/HSF1 downstream

0.203

128.2

0.5803

0.024

1.5–9.7

29

22

14

HOL

PY(2)

1.5–2.1

31

1,801,116

rs109421300

DGAT1 intron/HSF1 downstream

0.203

22.3

− 0.231

0.023

1.5–3.0

31

22

14

HOL

PC(3)

1.5–2.2

25

1,801,116

rs109421300

DGAT1 intron/HSF1 downstream

0.203

121.1

0.5048

0.022

1.5–4.5

25

23

14

MON

FC(1)

12.4–12.8

0

12,601,610

rs207790129

Intergenic

0.04

11.5

0.583

0.084

12.4–12.8

0

24

14

HOL

FC(3)

65.4–67.4

6

66,419,482

rs211058631

FBXO43 upstream/POLR2K upstream

0.11

13.3

− 0.257

0.034

65.3–67.5

6

24

14

HOL

MY(3)

65.3–67.4

6

66,326,942

rs110125070

SPAG1 intron

0.147

13.4

0.2125

0.028

64.5–68.1

6

24

14

HOL

PC(5)

65.3–67.4

6

66,326,942

rs110125070

SPAG1 intron

0.147

35.7

− 0.334

0.027

63.6–69.7

6

25

15

HOL

PC(1)

27.9–29.2

10

28,802,897

rs207905326

Intergenic

0.21

8.4

0.153

0.026

27.9–29.2

10

26

16

MON

PC(1)

60.3–60.9

1

60,618,083

rs43317278

Intergenic

0.34

8.7

0.194

0.032

60.3–60.9

1

27

19

HOL

FC(1)

51.3–51.4

2

51,321,632

rs109042366

CCDC57 intron

0.32

14.0

0.174

0.022

51.3–51.4

2

27

19

HOL

FY(1)

51.3–51.4

2

51,323,848

rs41921170

CCDC57 intron

0.318

10.9

0.1618

0.024

51.3–51.4

2

28

20

HOL

FY(1)

7.5–7.8

1

7661,288

rs467849681

ARHGEF28 intron

0.02

8.6

0.341

0.057

7.5–7.8

1

28

20

HOL

PY(1)

7.5–7.7

1

7339,763

rs455099807

Intergenic

0.001

8.3

1.0799

0.185

7.5–7.7

1

29

20

HOL

PC(1)

29.3–30.1

1

30,031,902

rs211443146

Intergenic

0.22

11.7

− 0.199

0.028

29.3–30.1

1

30

20

HOL

PC(3)

31.2–33.2

6

32,254,539

rs209333496

Intergenic

0.2

29.6

− 0.357

0.031

31.1–34.3

16

30

20

HOL

MY(1)

31.2–33.2

5

32,265,342

rs41943564

Intergenic

0.197

8.2

0.1864

0.032

31.2–33.2

5

30

20

HOL

FC(3)

31.3–32.6

2

32,296,239

rs210730645

Intergenic

0.201

17.4

− 0.274

0.032

31.1–34.3

2

31

22

MON

PC(1)

32.7–33.0

1

32,779,678

rs109419324

TAFA4 intron

0.01

8.5

− 0.701

0.118

32.7–33.0

1

32

27

MON

FC(1)

36.1–36.4

4

36,206,783

rs210205723

Intergenic

0.45

8.4

− 0.201

0.034

36.1–36.4

4

33

27

HOL

FC(1)

36.1–36.3

3

36,221,754

rs208624037

GPAT4 intron

0.38

11.1

− 0.149

0.022

36.1–36.3

3

34

27

NOR

FC(1)

36.1–36.4

3

36,301,028

rs383292923

ANK1 intron

0.34

9.1

− 0.197

0.032

36.1–36.4

3

35

29

HOL

PC(1)

9.0–9.7

2

9563,396

rs378183369

Intergenic

0.31

12.6

0.158

0.022

9.0–9.7

2

36.

29

HOL

PC(2)

41.4–43.4

12

42,393,898

rs211552605

LGALS12 upstream

0.15

11.6

− 0.226

0.032

41.4–44.2

30

  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. cConfidence interval (CI) of the most significant individual QTL
  5. dENSBTAG000000
  6. eEffect of the variant, expressed in genetic standard deviation units
  7. fExtended confidence interval (CI) encompassing all the individual QTL detected in the same genomic region
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Genetics Selection Evolution

ISSN: 1297-9686