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Table 5 Reliability gains when adding real sequence variants to HD or 60 K

From: Selecting sequence variants to improve genomic predictions for dairy cattle

Trait

Reliability for PA (%)

Gain for HD SNPs only

Gain for HD SNPs + 481,904 candidate SNPsa

Gain for HD SNPs + 481,904 candidate SNPs + indels

Gain for 60 k SNPs only

Gain for 60 k SNPs + 16,648 candidate SNPsb,c

Milk

37.9

34.1

33.9 (−0.2)

33.9

34.3

35.7 (1.4)

Fat

37.9

33.7

34.0 (0.3)

33.4

34.3

35.1 (0.8)

Protein

37.9

27.9

27.0 (−0.9)

26.7

27.5

28.2 (0.7)

Fat percentage

37.9

49.2

52.7 (3.5)

52.4

52.9

54.8 (1.9)

Protein percentage

37.9

42.1

41.6 (0.5)

43.0

41.6

44.3 (2.7)

Productive life

32.0

36.1

35.8 (−0.3)

36.4

35.6

38.2 (2.6)

Somatic cell score

34.7

35.9

36.1 (0.2)

37.1

35.1

37.0 (1.9)

Daughter pregnancy rate

31.5

30.8

30.0 (−0.8)

31.2

29.0

33.0 (4.0)

Cow conception rate

29.8

28.7

28.1 (−0.6)

28.8

28.9

31.8 (2.9)

Heifer conception rate

30.0

19.0

20.3 (1.3)

19.7

20.5

21.5 (1.0)

Sire calving ease

29.9

27.8

27.7 (−0.1)

25.2

24.5

28.5 (4.0)

Daughter calving ease

25.3

32.5

30.8 (−1.7)

29.9

31.5

31.4 (−0.1)

Sire stillbirth

29.0

7.6

7.3 (−0.3)

7.1

7.6

7.8 (0.2)

Daughter stillbirth

23.8

37.4

37.0 (−0.4)

35.8

35.4

38.0 (2.6)

Final score

36.2

24.7

25.5 (0.8)

25.8

24.6

27.8 (3.2)

Stature

38.2

30.4

32.4 (2.0)

32.8

30.3

34.7 (4.3)

Strength

37.4

29.9

31.8 (1.9)

31.8

29.9

34.5 (4.6)

Dairy form

37.4

33.8

35.3 (1.5)

35.8

35.0

38.2 (3.2)

Foot angle

36.7

17.3

17.6 (0.3)

18.2

17.2

19.6 (2.4)

Rear legs (side view)

37.3

21.9

22.7 (0.8)

22.0

22.1

24.1 (2.0)

Body depth

37.6

31.0

33.1 (2.1)

33.7

31.2

36.0 (4.8)

Rump angle

37.8

32.7

34.0 (1.3)

33.5

32.9

36.1 (3.2)

Rump width

37.1

29.2

30.4 (1.2)

30.2

29.1

32.5 (3.4)

Fore udder attachment

37.5

35.1

36.4 (1.3)

36.1

35.0

39.0 (4.0)

Rear udder height

37.3

24.7

25.7 (1.0)

25.8

24.1

27.3 (3.2)

Udder depth

38.0

40.2

42.6 (2.4)

42.8

40.6

44.6 (4.0)

Udder cleft

37.1

23.7

24.5 (0.8)

24.0

23.6

25.5 (1.9)

Front teat placement

37.6

32.6

33.4 (0.8)

32.3

30.9

35.0 (4.1)

Teat length

37.7

29.0

30.3 (1.3)

29.9

28.0

32.7 (4.7)

Rear legs (rear view)

36.0

20.7

20.3 (−0.4)

20.1

20.4

22.8 (2.4)

Feet and leg score

36.4

16.9

16.5 (−0.4)

16.6

15.9

18.3 (2.4)

Rear teat placement

37.4

33.1

33.6 (0.5)

32.1

32.9

35.2 (2.3)

Net merit

34.4

23.8

24.3 (0.5)

24.4

23.4

24.7 (1.3)

Average

35.2

28.8

29.4 (0.6)

29.2

29.5

32.2 (2.7)

  1. Reliability gains in percentage points over parent average reliability
  2. PA parent average
  3. aDifference from reliability gain for HD SNPS only in parentheses
  4. bDifference from reliability gain for 60 k SNPS only in parentheses
  5. cDoes not include 6584 60 k markers that were not available in sequence data