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Table 6 QTL detected for udder 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

37

1

HOL

US(1)

110.3–111.0

1

110,870,166

rs42324415

Intergenic

0.32

9.3

0.19

0.031

110.3–111.0

1

38

2

NOR

RUH(4)

6.0–6.7

2

6,237,254

rs385990556

Intergenic

0.02

16.5

− 1.185

0.14

4.5–9.2

11

39

4

HOL

UD(1)

10.0–10.2

0

10,126,995

rs42524022

Intergenic

0.36

8.5

0.131

0.022

10.0–10.2

0

40

4

HOL

FTD(1)

70.6–70.7

0

70,620,943

rs210515134

Intergenic

0.47

8.9

− 0.182

0.03

70.6–70.7

0

41

5

HOL

TL(1)

12.4–12.5

1

12,441,072

rs109808447

TMTC2 Intron

0.14

25

0.379

0.036

12.4–12.5

1

42

5

HOL

UD(1)

88.7–88.9

2

88,800,994

rs110461240

ABCC9 intron

0.45

12.4

0.186

0.026

88.7–88.9

2

42

5

HOL

FUA(1)

88.7–88.9

2

88,800,994

rs110461240

ABCC9 intron

0.457

11.3

0.1787

0.026

88.7–88.9

2

43

6

HOL

RUH(1)

71.9–72.2

0

72,022,013

rs136970036

Intergenic

0.28

14.9

0.272

0.034

71.9–72.2

0

44

6

MON

UD(1)

88.6–89.6

1

88,744,985

rs110181141

Intergenic

0.37

9.2

− 0.256

0.042

88.6–89.6

5

45

6

HOL

SCS(1)

88.4–89.2

3

88,881,928

rs474137839

Intergenic

0.31

9.2

0.206

0.033

88.4–89.2

3

45

6

HOL

UD(1)

88.4–89.2

4

88,697,293

rs110041776

GC intron

0.407

8.6

0.1789

0.03

88.4–89.2

4

46

8

HOL

FTD(2)

81.9–83.1

3

82,059,790

rs134625094

Intergenic

0.11

10.8

− 0.316

0.047

81.9–85.4

8

47

9

MON

SCS(1)

23.4–23.7

1

23,620,280

rs437752750

ME1 Intron

0.02

9.5

− 0.718

0.114

23.4–23.7

1

48

9

MON

SCS(1)

25.7–26.3

1

25,888,225

rs797068196

HEY2 upstream

0.02

9.1

− 0.78

0.127

25.7–26.3

1

49

9

MON

SCS(1)

28.1–29.2

1

28,197,098

rs455285205

38849d intron

0.01

8.2

− 0.859

0.147

28.1–29.2

1

50

14

MON

RUH(1)

24.4–25.1

3

25,052,440

rs210030313

PLAG1 5′UTR/CHCHD7 upstream

0.07

12.5

− 0.506

0.07

24.4–25.1

3

51

17

MON

FUA(1)

62.6–62.7

0

62,679,331

rs109168890

Intergenic

0.42

13.1

− 0.283

0.038

62.6–62.7

0

51

17

MON

US(1)

62.6–62.9

0

62,714,882

rs109332098

Intergenic

0.215

12.3

− 0.358

0.049

62.6–62.9

0

52

17

NOR

US(1)

62.5–62.9

2

62,694,032

rs109134926

Intergenic

0.21

10.0

− 0.272

0.042

62.5–62.9

2

53

19

HOL

MSS(1)

7.5–7.7

1

7,565,865

rs445450010

Intergenic

0.47

10.5

− 0.153

0.023

7.5–7.7

1

54

19

HOL

MSS(1)

59.3–60.4

0

60,151,690

rs109603247

Intergenic

0.18

8.9

0.186

0.031

59.3–60.4

0

55

19

MON

UD(1)

60.5–61.5

0

60,523,834

rs134785404

Intergenic

0.37

9.0

− 0.199

0.032

60.5–61.5

0

55

19

MON

MSS(1)

59.3–60.4

0

60,151,690

rs109603247

Intergenic

0.183

8.9

0.1856

0.031

59.3–60.4

0

56

20

HOL

FUA(3)

26.1-28.0

2

27,082,437

rs209792391

Intergenic

0.29

10.9

− 0.192

0.028

25.6––28

3

57

24

MON

UB(1)

33.2–35.3

11

34,288,737

rs382921722

Intergenic

0.4

9.1

0.326

0.053

33.2–35.3

11

58

24

HOL

RUH(1)

33.3–34.6

3

34,310,163

rs482718265

Intergenic

0.04

10.5

− 0.377

0.057

33.3–34.6

3

59

26

HOL

TO(1)

38.5–38.9

2

38,725,076

rs133440951

Intergenic

0.05

8.6

− 0.302

0.051

38.5–38.9

2

60

28

MON

MSS(1)

19.3–21.1

4

20,158,547

rs43101108

Intergenic

0.09

8.7

− 0.342

0.057

19.3–21.1

4

61

29

HOL

UD(3)

49.1–50.3

4

49,421,004

rs208859984

KCNQ1 Intron

0.31

12.7

− 0.167

0.023

49.1–51.5

24

61

29

HOL

SCS(1)

49.3–50.3

4

49,782,986

rs437410319

KCNQ1 Intron

0.066

8.4

0.2493

0.042

49.3–50.3

4

61.

29

HOL

UB(2)

48.3–50.3

8

49,299,622

rs210749543

NAP1L4 Intron

0.052

10.8

− 0.347

0.051

48.3–51.2

8

  1. #: number of
  2. aID number associated with a group of QTL linked with udder traits that had overlapping confidence intervals or less than 1 Mbp distance between the bounds of the confidence intervals
  3. bIndividual QTL; somatic cell score (SCS), clinical mastitis score (CM), udder support (US), udder depth (UD), fore udder attachment (FUA), rear udder height (RUH), fore teat distance (FTD), udder balance (UB), teat orientation (TO), teat length (TL), and milking speed score (MSS)
  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