Reliability genomic selection

Genomics breeding value excellent prediction tool Article previously published in the independent farmers weekly “Boerderij�

The breeding value of bulls based on their daughters hardly deviates from their genomic breeding value.

The level of individual traits is also unaffected.

In breeding circles genomics is a trending topic. However, it

The debate focuses on whether the genomic breeding value

is nothing more than a method that provides extra information

(gBv) is reliable enough to allow young bulls to already be

in addition to the expectation value given to young bulls that

used as sires based on this value. To investigate whether

is derived from the breeding values of their sire and dams.

and how the genomic breeding values alter, CRV compared

And, as figures from CRV reveal, that system functions very

the last breeding values of 322 bulls with their own genomic

well, as the breeding value based on daughters hardly

breeding value. 64 of these bulls were awarded their first

deviates from the genomic breeding value. The genetic

breeding value in December 2010; 97 in April 2011; 87 in

information boosts the reliability of the expectation values

August 2011 and 74 in December 2011. The average reliability

from 35 percent to some 60 percent (see graph).

of the breeding values of all these bulls (based on daughters)

Using markers the employees at the Animal Evaluation Unit

is 78 percent.

process the genetic data of traits using a plus or minus on the expectation values. This increases the reliability of the

Genomic breeding value retains its worth

breeding value to some 60 percent, and later on up to 75

Firstly, it appears that the average breeding value based

percent when the first breeding value based on daughters

on daughters is around the figure indicated by the genomic

follows. As the number of daughters increases, the reliability

breeding value. The second graph below shows for the total

increases with each successive index.

conformation trait that with bulls noting a genomic breeding

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Genomics breeding value excellent prediction tool

value of 105 will have breeding value figures between 100

CRV determines these differences for several traits (table 3).

and 110 based on their daughters. As the level rises or falls,

The very slight deviation per trait is striking. Analysis shows

the deviation remains more or less the same; but does shift

that 70 to 90 percent of the bulls will be placed in the same

in line with the values. In other words: a bull with a genomic

class or higher based on their genomic breeding values, as

breeding value of 101 will never be given a breeding value of

they would be based on the daughters. There is a degree of

113 for total conformation based on daughters, or vice versa.

variation, but the risk of being disappointed is small.

For Theo Gieling, international breeding specialist at CRV, this represents a breakthrough. „You see that the average

Young breeding bull or genomics bull

level corresponds, but also if examined at trait level, the

In practice, farmers are not afraid of huge differences

bull performs at the same level he scores with his genomic

between the classic breeding values compared with the

breeding value.� And it’s not just the extreme figures that

genomic values. According to Gieling, approximately 35

count. In the upper right of the table at breeding value NVI (in

percent of all inseminations using CRV bulls are already done

English: Dutch-Flemish Index) the number of bulls is shown

using InSire animals (young bulls with a genomic breeding

that fall in a certain class genomically as well as being in the

value). 65 percent of them are InSire Top Bulls; specially

same class with their breeding value based on daughters.

selected young bulls that are available separately on the

Roughly half of the bulls stay in the same class. About a

CRV bull chart. Many farmers already opt for bulls with a first

quarter is relegated to a lower class, while another quarter

or second breeding value of some 75 percent reliability.

is promoted to a higher class. For the individual traits too,

Even so, Gieling says that farmers should remain alert and

the average of the last breeding value per level is virtually

not rely on a single bull. The individual breeding value has

identical to the level of the genetic breeding value calculated

a reliability of 60 percent; the ultimate breeding value may

earlier. A number of examples of this are shown in table 3.

differ. If the aim is higher milk production and you select a

For instance, 85 bulls in the class 15-24 kg protein have an

group of bulls that inherit a lot of milk, you will get daughters

average genomic breeding value of 19.1 kg protein. Based

that also perform well in that area too. For bulls with a high

on the daughter information, these same 85 bulls arrive at an

positive status for milk based on their average genomic

average of 20.6 kg protein. The total shows that the breeding

breeding value, will show the same profile when they have

value of 321 bulls based on daughter only deviates by just

breeding values based on daughters.

0.8 kg protein.

Author: Wynand Hogenkamp

First breeding value stays close to genomic breeding value

reliability of breeding values (in %) with bulls at different ages

comparison of genomic breeding value with last breeding value based on daughters for total conformation trait

most recent breeding value

Increasing reliability

100 80 60 40 20 0

test bull

genomic proven proven bull bull (1st yr.) bull

115 110 100 95 90 0

96

98

100

102

104

106

108

110

112

114

genomic breeding value

The reliability of the breeding value of young bulls increases as CRV uses the genetic data of the animal itself alongside the parent data (left). The reliability increases as soon as daughter data becomes available. The second graph shows that the average breeding value based on daughters is around the figure indicated by the genomic breeding value.

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Genomics breeding value excellent prediction tool

1. Majority of bulls stay in same class comparison of shift in class of genomic breeding value compared with last breeding value based on daughter for NVI trait NVI genomics NVI daughters

-100 – 51

-50 – 1

0 – 49

-100 – 51

1

3

3

-50 – 1

1

8

16

4

0 – 49

1

15

38

23

3

4

21

66

23

1

115

7

22

39

4

72

3

11

3

1

18

118

76

8

1

321

50 – 99 100 – 149 150 – 199 totaal

3

30

85

50 – 99

100 – 149

150 – 199

200 – 249

totaal 7 29 80

The majority of bulls that fall in a certain class based on genomic breeding value, would also fall into the same class using the breeding values based on daughters.

2. Difference in breeding values small

3. Averages show practically no shift

last breeding value with daughter data compared with genomic breeding value trait difference

comparison of the various classes within three traits number of bulls

genomics

daughters

95 – 99

13

98.2

97.2

100 – 104

147

102.3

102.0

105 – 109

138

106.6

105.9

110 – 114

24

110.6

110.0

Total/av.

322

104.6

104.1

-50 – 0

55

-21

-13

0 – 50

142

27

34

50 – 100

101

72

75

100 – 150

21

120

107

Total/av.

319

40

45

9

-7.9

-8.9

Trait

Difference

class

Reliability NVI

+17.1

Total conf.

NVI

+1.4

Kg milk

-2.9

Kg fat

+1.6

Kg protein

+0.8

Longevity

-12.6

Total conformation

-0.5

Frame

-0.6

Dairy strength

-0.4

Udder

-0.3

Feet and legs

-0.3

Somatic cell count

+0.1

Fertility index

+0.2

The average breeding value based on daughter data (rel. = 78 %) is slightly better for NVI, kg fat and kg protein than the calculation based on the genomic information (rel. = 61 %).

Inet

Kg protein -15 – -6 -5 – 4

49

-0.2

0.9

5 – 14

98

9.9

11.8

15 – 24

85

19.1

20.6

25 – 34

56

29.0

27.3

34 – 44

20

38.2

37.2

45 – 54

4

50.0

55.0

Total/av.

321

15.9

16.7

The average value determined based on genomic traits is practically identical to the average value based on daughter data.

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