2006 j.b. cole animal improvement programs laboratory agricultural research service, usda,...
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2006
J.B. ColeJ.B. Cole
Animal Improvement Programs LaboratoryAgricultural Research Service, USDA, Beltsville, [email protected]
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
CSU 2006 – Breeding and Genetics Seminar (9) Cole200
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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
CSU 2006 – Breeding and Genetics Seminar (13) Cole200
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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
CSU 2006 – Breeding and Genetics Seminar (14) Cole200
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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
CSU 2006 – Breeding and Genetics Seminar (17) Cole200
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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
CSU 2006 – Breeding and Genetics Seminar (19) Cole200
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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
CSU 2006 – Breeding and Genetics Seminar (23) Cole200
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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
CSU 2006 – Breeding and Genetics Seminar (24) Cole200
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HeritabilitiesHeritabilities
Calving Ease (Direct)8.6%
Calving Ease (MGS) 3.6%
Stillbirth (Direct)3.0%
Stillbirth (MGS) 6.5%
CSU 2006 – Breeding and Genetics Seminar (25) Cole200
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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
CSU 2006 – Breeding and Genetics Seminar (26) Cole200
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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
CSU 2006 – Breeding and Genetics Seminar (32) Cole200
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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