Table 1

Distribution of the top 100 most significant SNP effects for predicted transmitting abilities for 13 production, health, and reproduction traits of contemporary U.S. Holsteins by chromosome.

Chr

MY

FY

PY

FPC

PPC

PL

SCS

DPR

SCE

DCE

SSB

DSB

NM

All traits


1

2

4

4

4

5

15

4

17

7

6

7

3

15

93

2

3

0

0

0

1

1

11

2

0

0

0

2

0

20

3

10

4

1

4

1

9

7

17

4

0

4

6

1

68

4

3

2

2

0

0

4

0

0

2

0

3

0

0

16

5

2

2

2

7

13

0

4

0

7

3

10

0

2

52

6

2

2

5

1

6

2

9

0

0

6

0

1

5

39

7

0

6

1

1

2

11

13

15

4

11

0

6

4

74

8

2

1

0

0

0

4

1

3

0

0

0

3

1

15

9

7

6

1

1

2

0

0

0

4

3

1

6

4

35

10

5

0

0

0

3

0

2

6

1

0

4

0

0

21

11

3

3

3

1

3

0

1

0

1

0

0

5

0

20

12

2

1

1

2

3

0

6

0

8

2

6

1

1

33

13

13

12

8

4

1

0

1

2

1

0

0

7

4

53

14

2

1

1

24

2

0

0

2

0

0

6

4

0

42

15

1

2

1

2

0

1

0

0

1

1

4

5

1

19

16

1

0

0

0

0

2

11

1

0

0

3

3

0

21

17

4

7

6

11

14

9

1

5

20

21

7

2

14

121

18

8

4

6

5

4

8

2

5

9

12

6

4

10

83

19

2

3

2

0

0

0

0

0

0

0

0

3

0

10

20

0

2

11

0

2

0

2

0

1

1

1

5

0

25

21

4

1

5

0

5

0

0

0

2

1

6

5

1

30

22

1

0

0

0

0

3

2

3

0

1

0

2

1

13

23

5

5

9

2

3

0

1

0

2

1

1

16

3

48

24

2

1

2

2

2

1

1

0

1

1

3

0

2

18

25

0

2

0

3

0

0

5

1

0

0

1

0

0

12

26

0

7

6

6

10

9

3

4

6

10

9

1

11

82

27

5

6

7

0

1

1

1

0

3

1

0

1

3

29

28

0

0

5

0

1

2

0

3

3

1

1

1

3

20

29

0

0

0

0

0

1

2

1

0

2

1

3

1

11

X

11

16

11

19

16

15

9

12

12

16

15

3

12

167

U

0

0

0

1

0

2

1

1

1

0

1

2

1

10

P*

10-12

10-24

10-23

10-17

10-22

10-29

10-23

10-25

10-38

10-23

10-24

10-21

10-34

R2

0.42

0.43

0.42

0.45

0.40

0.54

0.54

0.53

0.52

0.42

0.56

0.55

0.49


SNP, single nucleotide polymorphism; Chr, chromosome; MY, milk yield; FY, fat yield; PY, protein yield; FPC, fat percentage; PPC, protein percentage; PL, productive life; SCS, somatic cell score; DPR, daughter pregnancy rate; SCE, service-sire calving ease; DCE, daughter calving ease; SSB, service-sire stillbirth; DSB, daughter stillbirth; NM, net merit; 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