2006 j.b. cole animal improvement programs laboratory agricultural research service, usda,...

2006

J.B. ColeJ.B. Cole

Animal Improvement Programs LaboratoryAgricultural Research Service, USDA, Beltsville, MDjcole@aipl.arsusda.gov

Genetic Evaluation of Genetic Evaluation of Calving Traits in US Calving Traits in US

HolsteinsHolsteins

CSU 2006 – Breeding and Genetics Seminar (2) Cole200

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IntroductionIntroduction

A national evaluation was implemented for calving ease (CE) in August 2002 and for stillbirth (SB) for Holstein in August 2006.

A calving ability index (CA$) which includes SB and calving ease (CE) was developed.

Some challenges with the CE and SB evaluations remain

CSU 2006 – Breeding and Genetics Seminar (5) Cole200

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Calving Ease DefinitionCalving Ease Definition

Reported on a five-point scale:

1 = No problem

2 = Slight problem

3 = Needed assistance

4 = Considerable force

5 = Extreme difficulty

Scores of 4 and 5 are combined

CSU 2006 – Breeding and Genetics Seminar (6) Cole200

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Stillbirth DefinitionStillbirth Definition

Reported on a three-point scale:

Scores of 2 and 3 are combined

1 = calf born alive,

2 = calf born dead,3 = calf died within 48 h of parturition.

CSU 2006 – Breeding and Genetics Seminar (7) Cole200

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Distribution of Stillbirth and Distribution of Stillbirth and Calving Ease ScoresCalving Ease Scores

7,484,309 29,320348,6775,348,0291,758,283Total

96,087 1,27232,19638,92923,6905

207,242 1,74037,851108,03759,6144

633,029 3,35370,522375,203183,9513

738,853 2,53749,858482,720203,7382

5,809,09820,418158,2504,343,1401,287,2901

Total3210

Calv

ing

Ease

Sco

re

Stillbirth Score

CSU 2006 – Breeding and Genetics Seminar (8) Cole200

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Stillbirth Records by LactationStillbirth Records by Lactation

0

100

200

300

400

500

1980 1990 2000

Birth Year

Num

ber

of R

ecor

ds (

thou

sand

s)

3

2

1

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Detecting Stillbirth Data Detecting Stillbirth Data ErrorsErrors

0

5

10

15

Birth Year

Perc

enta

ge

%SB

%DB

CSU 2006 – Breeding and Genetics Seminar (10) Cole200

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Data and EditsData and Edits 7 million SB records were available

for Holstein cows calving since 1980 Herds needed ≥10 calving records

with SB scores of 2 or 3 for inclusion

Herd-years were required to include ≥20 records

Only single births were used (no twins)

CSU 2006 – Breeding and Genetics Seminar (11) Cole200

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Sire-MGS Threshold ModelSire-MGS Threshold Model

Implemented for calving ease (Aug 2002) and stillbirth (Aug 2006)

Sire effects allow for corrective matings in heifers to avoid large calves

MGS effects control against selection for small animals which would have difficulty calving

CSU 2006 – Breeding and Genetics Seminar (12) Cole200

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Genetic Evaluation ModelGenetic Evaluation Model

A sire-maternal grandsire (MGS) threshold model was used:• Fixed: year-season, parity-sex, sire

and MGS birth year• Random: herd-year, sire, MGS

(Co)variance components were estimated by Gibbs sampling• Heritabilities are 3.0% (direct) and

6.5% (MGS)

ijklnoprnplonlkjiijklnopr e m s BM BS PS YS hy y ijklnoprnplonlkjiijklnopr e m s BM BS PS YS hy y ijklnoprnplonlkjiijklnopr e m s BM BS PS YS hy y

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Trait DefinitionTrait Definition

PTA are expressed as the expected percentage of stillbirths Direct SB measures the effect of

the calf itself Maternal SB measures the effect

of a particular cow (daughter) A base of 8% was used for both

traits: Direct: bulls born 1996–2000 Maternal: bulls born 1991–1995

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Phenotypic Trend for Phenotypic Trend for StillbirthsStillbirths

0

2

4

6

8

10

12

14

1980

1983

1986

1989

1992

1995

1998

2001

2004

Birth Year

% St

illbi

rth

HeifersCowsAll animals

CSU 2006 – Breeding and Genetics Seminar (15) Cole200

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Genetic Trend for StillbirthsGenetic Trend for Stillbirths

5.0

6.0

7.0

8.0

9.0

10.0

1980 1985 1990 1995 2000Birth Year

%SB

H

Direct

Maternal

CSU 2006 – Breeding and Genetics Seminar (16) Cole200

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Distribution of PTADistribution of PTA

0

5

10

15

20

25

30

35

40

6.1-

6.5

6.6-

7.0

7.1-

7.5

7.6-

8.0

8.1-

8.5

8.6-

9.0

9.1-

9.5

9.6-

10.0

10.1-10.

5

10.6-11.

0

11.1-11.

5

11.6-12.

0>1

2.0

%SBH

Perc

ent

of S

core

s Direct

Maternal

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Distribution of ReliabilitiesDistribution of Reliabilities

0

5

10

15

20

25

30

35

40

45

50

41-4

5

46-5

0

51-5

5

56-6

0

61-6

5

66-7

0

71-7

5

76-8

0

81-8

5

86-9

0

91-9

5

96-9

9

Reliability

Perc

enta

ge

Direct

Maternal

CSU 2006 – Breeding and Genetics Seminar (18) Cole200

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Dystocia and StillbirthDystocia and Stillbirth

Meyer et al. (2001) make a strong argument for the inclusion of dystocia in models for SB

Difficulty of interpretation - formidable educational challenge

Interbull trait harmonization - none of the March 2006 test run participants included dystocia in their models

Changes in sire and MGS solutions on the underlying scale between models were small

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Evaluation ConclusionsEvaluation Conclusions

Reliabilities for SB averaged 45% versus 60% for CE

Phenotypic and genetic trends from 1980 to 2005 were both small

An industry-wide effort is underway to improve recording of calf livability

CSU 2006 – Breeding and Genetics Seminar (20) Cole200

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Index DataIndex Data 7 million SB records were

available for Holstein cows calving since 1980

Calvings with unknown MGS were eliminated for VCE

Records with sire and MGS among the 2,600 most-frequently appearing bulls were selected

CSU 2006 – Breeding and Genetics Seminar (21) Cole200

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Data (cont’d)Data (cont’d) Herds needed ≥10 calving records

with SB scores of 2 or 3 in the database to be included

Herd-years were required to include ≥20 records and only single births were used

Inclusion of all records for a cow was not guaranteed

The final dataset included 2,083,979 calving records from 5,765 herds and 33,304 herd-years

CSU 2006 – Breeding and Genetics Seminar (22) Cole200

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SamplingSampling Six datasets of Six datasets of ~250,000~250,000 records each records each

were created by randomly sampling were created by randomly sampling herd codes without replacementherd codes without replacement

Datasets ranged from Datasets ranged from 239,192239,192 to to 286,794286,794 observations, and all averaged observations, and all averaged 7%7% stillbirths stillbirths

A common pedigree file was used to A common pedigree file was used to facilitate comparisons between sire facilitate comparisons between sire and MGS solutionsand MGS solutions

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Bayesian (co)variance Bayesian (co)variance components estimatescomponents estimates

Var(Sire) Var(MGS)Cov(S-MGS)

Sample

Mean SD

Mean SD

Mean SD

10.01

0 0.0020.01

8 0.0020.00

40.00

1

20.00

7 0.0020.01

7 0.0020.00

50.00

1

30.00

9 0.0010.01

9 0.0020.00

50.00

1

40.00

8 0.0010.01

9 0.0020.00

40.00

1

50.00

8 0.0010.01

8 0.0020.00

20.00

1

60.00

9 0.0020.01

7 0.0020.00

40.00

1

Mean0.00

9 0.0020.01

8 0.0020.00

40.00

1

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HeritabilitiesHeritabilities

Calving Ease (Direct)8.6%

Calving Ease (MGS) 3.6%

Stillbirth (Direct)3.0%

Stillbirth (MGS) 6.5%

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Genetic Correlations Among SB Genetic Correlations Among SB and CEand CE

Trait

CE SB

DirectMaternal

Direct

Maternal

CEDirect 1.00 0.46 0.67 0.25

Maternal 1.00 0.29 0.63

SBDirect 1.00 0.28

Maternal 1.00

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Economic AssumptionsEconomic Assumptions

Newborn calf value

Expenses per difficult birth (CE ≥4)

$450 for females

$150 for males

$75 labor and veterinary

$100 reduced milk yield

$75 reduced fertility and longevity

1.5% chance of cow death ($1800)

CSU 2006 – Breeding and Genetics Seminar (27) Cole200

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Calving Ability IndexCalving Ability Index

CA$ has a genetic correlation of 0.85 with the combined direct and maternal CE values in 2003 NM$ and 0.77 with maternal CE in TPI

Calving traits receive 6% of the total emphasis in NM$ (August 2006 revision)

(DCE ) (MCE ) (DSB ) (MSCA$ B ) 4 8 3 8 4 8 8 8

CSU 2006 – Breeding and Genetics Seminar (28) Cole200

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Breeds Other Than HolsteinBreeds Other Than Holstein

Brown Swiss economic values are −6 for SCE and −8 for DCE• Separate SB evaluations are

not available• CE values include the

correlated response in SB

Other breeds will be assigned CA$ of 0

CSU 2006 – Breeding and Genetics Seminar (29) Cole200

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Calving Ease Genetic Calving Ease Genetic CorrelationsCorrelations

Service sire above diagonal, daughter belowService sire above diagonal, daughter below

Ctry CAN DNK

FRA ITA NLD

SWE

USA

CAN .87 .81 .70 .80 .86 .75

DNK

.84 .93 .77 .86 .96 .90

FRA .80 .80 .74 .84 .91 .88

ITA .58 .59 .85 .60 .70 .61

NLD .89 .81 .79 .59 .89 .79

SWE

.75 .82 .89 .78 .69 .86

USA .71 .78 .93 .76 .77 .87

CSU 2006 – Breeding and Genetics Seminar (30) Cole200

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Stillbirth Genetic Stillbirth Genetic CorrelationsCorrelations

Service sire above diagonal, daughter belowService sire above diagonal, daughter below

Ctry DNK

FIN ISR NLD SWE

USA

DNK

.85 .82 .67 .92 .70

FIN .82 .77 .64 .82 .65

ISR .67 .70 .73 .80 .66

NLD .82 .77 .60 .65 .63

SWE

.88 .92 .65 .73 .64

USA .81 .87 .60 .71 .87

CSU 2006 – Breeding and Genetics Seminar (31) Cole200

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Brown Swiss Calving Ease Brown Swiss Calving Ease Service sire correlations above diagonal, Service sire correlations above diagonal,

daughter belowdaughter below

Ctry CHE DEU

NLD

USA

CHE .83 .81 .68

DEU .61 .77 .67

NLD .89 .76 .79

USA .70 .61 .76

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Index ConclusionsIndex Conclusions

A routine evaluation for stillbirth in US Holsteins was implemented in August 2006

Direct and maternal stillbirth were included in NM$ for Holsteins starting in August 2006

August 2006 data were included in the September 2006 Interbull test run

The US will participate in routine Interbull evaluations beginning in November 2006

CSU 2006 – Breeding and Genetics Seminar (33) Cole200

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Recent Calving Ease Recent Calving Ease ResearchResearch

CSU 2006 – Breeding and Genetics Seminar (34) Cole200

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Abnormal Herd-YearsAbnormal Herd-Years

Many herd-years have abnormal distributions of scores

Two recent approaches to problem• Eliminate HY based on GoF tests• Collapse categories when mode > 1

Both strategies improve prediction of later evaluations by earlier

CSU 2006 – Breeding and Genetics Seminar (35) Cole200

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An IllustrationAn Illustration Herds with unusual distributions of data affect

evaluations of bulls

Worst case is when large share of records for a bull are in one “bad” herd

Herd reporting changes over time

0

20

40

60

80

100

1 2 3 4 5

Calving Ease Scores - Herd 1

Scor

e by

Her

d (%

)

Parity 1Parity 2

0

20

40

60

80

100

1 2 3 4 5

Calving Ease Scores - Herd 2

Scor

e by

Her

d (%

)

CSU 2006 – Breeding and Genetics Seminar (36) Cole200

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Test Edits - Test Edits - 22 GoF statisticsGoF statistics

Based on multinomial distributions

Independent of herd size

2

i i,1 i,2 i,3 i,4 i,5

i 1 i

Log(Multi(N,n ,n ,n ,n ,n ,P))GoF

N

CSU 2006 – Breeding and Genetics Seminar (37) Cole200

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Percentage of Score by Parity Percentage of Score by Parity In All (AN) and GoF Excluded In All (AN) and GoF Excluded

(AG) Herds(AG) Herds

0102030405060708090

100

1 2 3 4 5

Calving Ease Score

Cou

nts

by H

erd

-Pari

ty (

%)

Parity 1 - AN

Parity 2 - AN

Parity 1 - AG

Parity 2 - AG

CSU 2006 – Breeding and Genetics Seminar (38) Cole200

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Collapse CategoriesCollapse Categories

The mode for CE scores in a herd is expected to be 1, but was higher for nearly 10% of data

Data from herd-years with a mode of 4 or 5 (1.2%) were deleted

A mode of 3 is assumed to indicate that the scorer normalized the data (middle score of 3 for an 'average' birth)

CSU 2006 – Breeding and Genetics Seminar (39) Cole200

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Collapse CategoriesCollapse Categories

Herds with a mode of 2 or 3: scores up to the mode were changed to 1, and scores greater than the mode were decreased accordingly

Herd-years with a mode of 3: scores 1-3 all become 1, scores of 4 are changed to 2, and scores of 5 are changed to 3

Combining categories lowered the portion of difficult calvings and increased the impact of the subsequent goodness-of-fit test

Overall, 6.4% of data were excluded

CSU 2006 – Breeding and Genetics Seminar (40) Cole200

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ConclusionsConclusions

Exclusion of herds with poor distributions improves prediction of future evaluations across birth years • Correlations across all data

increased from .66 to .68 Herds with poor score

distributions were excluded uniformly across herd size

Exclusion of herds results in loss of evaluations for some bulls

CSU 2006 – Breeding and Genetics Seminar (41) Cole200

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Separate Parity EffectsSeparate Parity Effects

First and later parities currently modelled as a single trait

cblup90iod only accepts one threshold trait

Options for bivariate analysis• Gibbs sampling (thrgibbs1)• Linearization (airemlf90)• RR on parity (cblup90iod)

CSU 2006 – Breeding and Genetics Seminar (42) Cole200

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ResultsResults

RR on a 0-1 parity effect does not account for heterogeneous variances

GS and AIREML solutions were similar• GS required more processing time than is

desirable for routine national evaluations• The impact of the approximation necessary

to linearize the scores is not known

Implementation of a bivariate analysis is desirable, but challenging

CSU 2006 – Breeding and Genetics Seminar (43) Cole200

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AcknowledgmentsAcknowledgments

Jeff Berger, Iowa State University John Clay, Dairy Records

Management Systems Ignacy Misztal and Shogo

Tsuruta, University of Georgia National Association of Animal

Breeders