Table 2

Distribution of the top 100 most significant SNP effects for predicted transmitting abilities for 18 conformation traits of contemporary U.S. Holsteins by chromosome.

Chr

STA

STR

BD

RW

DF

RA

FUA

RUH

UD

UC

FTP

RTP

TL

FA

RLS

RLR

FL

FS

All traits


1

3

3

3

1

5

2

3

5

5

4

2

7

8

3

12

1

2

3

72

2

1

1

1

1

4

5

3

11

1

5

6

10

2

0

6

7

5

3

72

3

1

4

0

1

10

2

1

1

3

3

1

2

2

0

7

0

0

0

38

4

3

3

0

1

0

1

1

1

1

0

8

1

7

1

0

4

2

2

36

5

8

6

14

5

0

12

7

4

7

0

4

1

6

7

4

3

11

9

108

6

0

6

3

10

0

7

9

5

2

8

14

5

4

5

2

3

5

8

96

7

2

2

0

0

11

0

5

5

5

13

7

7

2

0

3

0

0

5

67

8

1

1

1

1

6

16

0

0

0

4

1

1

1

1

1

0

1

0

36

9

1

0

1

0

0

14

2

0

1

1

7

5

0

3

0

0

0

0

35

10

7

1

10

14

19

4

12

21

4

3

2

4

0

0

1

0

0

16

118

11

30

13

23

2

6

2

4

15

2

5

0

4

13

4

1

32

11

16

183

12

3

0

0

0

1

3

0

0

3

3

1

3

5

0

4

0

1

3

30

13

3

13

9

5

2

1

4

1

3

1

4

3

1

8

1

4

9

1

73

14

0

0

1

0

5

0

0

1

0

3

1

0

0

1

2

1

2

0

17

15

1

2

1

2

0

2

1

0

3

6

0

5

0

2

0

0

1

0

26

16

1

3

4

8

5

2

7

2

4

1

8

7

3

2

10

2

1

3

73

17

1

1

0

0

3

0

2

0

6

1

2

1

15

15

6

1

5

0

59

18

0

0

0

0

0

3

0

0

1

1

0

2

3

7

8

1

2

0

28

19

3

2

2

10

1

1

7

3

4

8

4

5

0

0

0

1

0

5

56

20

7

5

4

1

0

0

7

3

7

1

4

3

0

10

1

9

3

2

67

21

1

0

0

2

0

0

2

1

9

4

5

1

9

2

3

1

2

1

43

22

1

2

2

2

2

5

2

1

3

1

3

1

2

1

4

2

4

3

41

23

2

1

1

1

1

1

2

2

2

2

4

1

0

0

1

0

0

2

23

24

0

0

0

0

2

0

0

0

2

1

1

2

3

1

4

0

0

0

16

25

0

2

2

0

2

0

1

0

3

1

1

1

0

2

0

1

1

1

18

26

3

7

2

4

2

2

8

4

11

1

1

1

4

13

5

9

16

5

98

27

0

0

0

0

1

0

1

0

2

10

0

6

0

0

3

0

1

0

24

28

1

0

0

0

0

0

1

2

0

0

4

1

0

0

0

0

1

1

11

29

0

0

0

1

0

4

0

0

0

1

1

1

0

2

1

0

1

0

12

X

14

22

15

27

12

9

8

10

6

7

2

9

10

10

7

18

12

10

208

U

2

0

1

1

0

2

0

2

0

1

2

0

0

0

3

0

1

1

16

P*

10-21

10-20

10-18

10-18

10-20

10-11

10-18

10-16

10-19

10-18

10-12

10-12

10-13

10-20

10-15

10-17

10-17

10-19

R2

0.56

0.49

0.48

0.53

0.45

0.40

0.56

0.50

0.55

0.52

0.48

0.46

0.39

0.52

0.38

0.47

0.49

0.56


SNP, single nucleotide polymorphism; Chr, chromosome; STA, stature; STR, strength; BD, body depth; RW, rump width; DF, dairy form; RA, rump angle; FUA, fore udder attachment; RUH, rear udder height; UD, udder depth; UC, udder cleft; FTP, front teat placement; RTP, rear teat placement; TL, teat length; FA, foot angle; RLS, rear legs (side view); RLR, rear legs (rear view); FL, feet/legs score; FS, final score; U, unknown. Boldface indicates ≥10 significant SNP effects. *Rounded cutoff for P value for top 100 most significant SNPs for trait. R2, variation accounted for by the top 100 SNPs for the trait.

Cole et al. BMC Genomics 2011 12:408   doi:10.1186/1471-2164-12-408

Open Data