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2006 J.B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD Genetic.

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Presentation on theme: "2006 J.B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD Genetic."— Presentation transcript:

1 2006 J.B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD jcole@aipl.arsusda.gov@aipl.arsusda.gov Genetic Evaluation of Calving Traits in US Holsteins

2 CSU 2006 – Breeding and Genetics Seminar (2) Cole 2006 Introduction  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

3 CSU 2006 – Breeding and Genetics Seminar (3) Cole 2006 History 1977 – NAAB-sponsored evaluations within AI organizations 1980 – NAAB-sponsored evaluations across AI organizations 1988 – Ordered categorical threshold model 1990 – Semiannual evaluations 1999 – Processing change from Iowa State University to USDA (November) 2002 – Sire-maternal grandsire (MGS) model

4 CSU 2006 – Breeding and Genetics Seminar (4) Cole 2006 Threshold model  Scores assumed to be observations on a continuous underlying scale  Thresholds estimated to relate observed scores to underlying scale Procedure allows for differences in amount of change between consecutive scores Observed scores Underlying scale 51 1 2345

5 CSU 2006 – Breeding and Genetics Seminar (5) Cole 2006 Calving 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

6 CSU 2006 – Breeding and Genetics Seminar (6) Cole 2006 Stillbirth 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.

7 CSU 2006 – Breeding and Genetics Seminar (7) Cole 2006 Distribution of Stillbirth and Calving Ease Scores 7,484,309 29,320348,6775,348,0291,758,283 Total 96,087 1,27232,19638,92923,690 5 207,242 1,74037,851108,03759,614 4 633,029 3,35370,522375,203183,951 3 738,853 2,53749,858482,720203,738 2 5,809,09820,418158,2504,343,1401,287,290 1 Total3210 Calving Ease Score Stillbirth Score

8 CSU 2006 – Breeding and Genetics Seminar (8) Cole 2006 Stillbirth Records by Lactation

9 CSU 2006 – Breeding and Genetics Seminar (9) Cole 2006 Detecting Stillbirth Data Errors

10 CSU 2006 – Breeding and Genetics Seminar (10) Cole 2006 Data 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)

11 CSU 2006 – Breeding and Genetics Seminar (11) Cole 2006 Sire-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

12 CSU 2006 – Breeding and Genetics Seminar (12) Cole 2006 Genetic 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)

13 CSU 2006 – Breeding and Genetics Seminar (13) Cole 2006 Trait 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

14 CSU 2006 – Breeding and Genetics Seminar (14) Cole 2006 Phenotypic Trend for Stillbirths

15 CSU 2006 – Breeding and Genetics Seminar (15) Cole 2006 Genetic Trend for Stillbirths

16 CSU 2006 – Breeding and Genetics Seminar (16) Cole 2006 Distribution of PTA

17 CSU 2006 – Breeding and Genetics Seminar (17) Cole 2006 Distribution of Reliabilities

18 CSU 2006 – Breeding and Genetics Seminar (18) Cole 2006 Dystocia 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

19 CSU 2006 – Breeding and Genetics Seminar (19) Cole 2006 Evaluation 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

20 CSU 2006 – Breeding and Genetics Seminar (20) Cole 2006 Index 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

21 CSU 2006 – Breeding and Genetics Seminar (21) Cole 2006 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

22 CSU 2006 – Breeding and Genetics Seminar (22) Cole 2006 Sampling  Six datasets of ~250,000 records each were created by randomly sampling herd codes without replacement  Datasets ranged from 239,192 to 286,794 observations, and all averaged 7% stillbirths  A common pedigree file was used to facilitate comparisons between sire and MGS solutions

23 CSU 2006 – Breeding and Genetics Seminar (23) Cole 2006 Bayesian (co)variance components estimates Var(Sire)Var(MGS)Cov(S-MGS) SampleMeanSDMeanSDMeanSD 10.0100.0020.0180.0020.0040.001 20.0070.0020.0170.0020.0050.001 30.0090.0010.0190.0020.0050.001 40.0080.0010.0190.0020.0040.001 50.0080.0010.0180.002 0.001 60.0090.0020.0170.0020.0040.001 Mean0.0090.0020.0180.0020.0040.001

24 CSU 2006 – Breeding and Genetics Seminar (24) Cole 2006 Heritabilities  Calving Ease (Direct)8.6%  Calving Ease (MGS)3.6%  Stillbirth (Direct)3.0%  Stillbirth (MGS)6.5%

25 CSU 2006 – Breeding and Genetics Seminar (25) Cole 2006 Genetic Correlations Among SB and CE Trait CESB DirectMaternalDirectMaternal CE Direct1.000.460.670.25 Maternal1.000.290.63 SB Direct1.000.28 Maternal1.00

26 CSU 2006 – Breeding and Genetics Seminar (26) Cole 2006 Economic 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)

27 CSU 2006 – Breeding and Genetics Seminar (27) Cole 2006 Calving 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)

28 CSU 2006 – Breeding and Genetics Seminar (28) Cole 2006 Breeds 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

29 CSU 2006 – Breeding and Genetics Seminar (29) Cole 2006 Calving Ease Genetic Correlations Service sire above diagonal, daughter below CtryCANDNKFRAITANLDSWEUSA CAN.87.81.70.80.86.75 DNK.84.93.77.86.96.90 FRA.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

30 CSU 2006 – Breeding and Genetics Seminar (30) Cole 2006 Stillbirth Genetic Correlations Service sire above diagonal, daughter below CtryDNKFINISRNLDSWEUSA 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

31 CSU 2006 – Breeding and Genetics Seminar (31) Cole 2006 Brown Swiss Calving Ease Service sire correlations above diagonal, daughter below CtryCHEDEUNLDUSA CHE.83.81.68 DEU.61.77.67 NLD.89.76.79 USA.70.61.76

32 CSU 2006 – Breeding and Genetics Seminar (32) Cole 2006 Index 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

33 CSU 2006 – Breeding and Genetics Seminar (33) Cole 2006 Recent Calving Ease Research

34 CSU 2006 – Breeding and Genetics Seminar (34) Cole 2006 Abnormal 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

35 CSU 2006 – Breeding and Genetics Seminar (35) Cole 2006 An 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

36 CSU 2006 – Breeding and Genetics Seminar (36) Cole 2006 Test Edits -  2 GoF statistics  Based on multinomial distributions  Independent of herd size

37 CSU 2006 – Breeding and Genetics Seminar (37) Cole 2006 Percentage of Score by Parity In All (AN) and GoF Excluded (AG) Herds 0 10 20 30 40 50 60 70 80 90 100 12345 Calving Ease Score Counts by Herd-Parity (%) Parity 1 - AN Parity 2 - AN Parity 1 - AG Parity 2 - AG

38 CSU 2006 – Breeding and Genetics Seminar (38) Cole 2006 Collapse 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)

39 CSU 2006 – Breeding and Genetics Seminar (39) Cole 2006 Collapse 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

40 CSU 2006 – Breeding and Genetics Seminar (40) Cole 2006 Conclusions  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

41 CSU 2006 – Breeding and Genetics Seminar (41) Cole 2006 Separate 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)

42 CSU 2006 – Breeding and Genetics Seminar (42) Cole 2006 Results  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

43 CSU 2006 – Breeding and Genetics Seminar (43) Cole 2006 Acknowledgments  Jeff Berger, Iowa State University  John Clay, Dairy Records Management Systems  Ignacy Misztal and Shogo Tsuruta, University of Georgia  National Association of Animal Breeders

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