Genetic Evaluation of Calving Traits in US Holsteins

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Presentation on genetic evaluation of calving traits made to the Department of Animal Science at Colorado State University.

Presentation on genetic evaluation of calving traits made to the Department of Animal Science at Colorado State University.

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  • 1. 200 6 J.B. ColeJ.B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD jcole@aipl.arsusda.gov Genetic Evaluation of CalvingGenetic Evaluation of Calving Traits in US HolsteinsTraits in US Holsteins
  • 2. CSU 2006 – Breeding and Genetics Seminar (2) Cole 200 6 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
  • 3. CSU 2006 – Breeding and Genetics Seminar (5) Cole 200 6 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
  • 4. CSU 2006 – Breeding and Genetics Seminar (6) Cole 200 6 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.
  • 5. CSU 2006 – Breeding and Genetics Seminar (7) Cole 200 6 Distribution of Stillbirth and CalvingDistribution of Stillbirth and Calving Ease ScoresEase Scores 7,484,30929,320348,6775,348,0291,758,283Total 96,0871,27232,19638,92923,6905 207,2421,74037,851108,03759,6144 633,0293,35370,522375,203183,9513 738,8532,53749,858482,720203,7382 5,809,09820,418158,2504,343,1401,287,2901 Total3210 CalvingEaseScore Stillbirth Score
  • 6. CSU 2006 – Breeding and Genetics Seminar (8) Cole 200 6 Stillbirth Records by LactationStillbirth Records by Lactation 0 100 200 300 400 500 1980 1990 2000 Birth Year NumberofRecords(thousands) 3 2 1
  • 7. CSU 2006 – Breeding and Genetics Seminar (9) Cole 200 6 Detecting Stillbirth Data ErrorsDetecting Stillbirth Data Errors 0 5 10 15 1980 1983 1986 1989 1992 1995 1998 2001 2004 Birth Year Percentage %SB %DB
  • 8. CSU 2006 – Breeding and Genetics Seminar (10) Cole 200 6 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)
  • 9. CSU 2006 – Breeding and Genetics Seminar (11) Cole 200 6 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
  • 10. CSU 2006 – Breeding and Genetics Seminar (12) Cole 200 6 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 emsBMBSPSYShyy +++++++= ijklnoprnplonlkjiijklnopr emsBMBSPSYShyy +++++++= ijklnoprnplonlkjiijklnopr emsBMBSPSYShyy +++++++=
  • 11. CSU 2006 – Breeding and Genetics Seminar (13) Cole 200 6 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
  • 12. CSU 2006 – Breeding and Genetics Seminar (14) Cole 200 6 Phenotypic Trend for StillbirthsPhenotypic Trend for Stillbirths 0 2 4 6 8 10 12 14 1980 1983 1986 1989 1992 1995 1998 2001 2004 Birth Year %Stillbirth Heifers Cows All animals
  • 13. CSU 2006 – Breeding and Genetics Seminar (15) Cole 200 6 Genetic Trend for StillbirthsGenetic Trend for Stillbirths 5.0 6.0 7.0 8.0 9.0 10.0 1980 1985 1990 1995 2000 Birth Year %SBH Direct Maternal
  • 14. CSU 2006 – Breeding and Genetics Seminar (16) Cole 200 6 Distribution of PTADistribution of PTA 0 5 10 15 20 25 30 35 40 6.1-6.56.6-7.07.1-7.57.6-8.08.1-8.58.6-9.09.1-9.59.6-10.010.1-10.510.6-11.011.1-11.511.6-12.0 >12.0 %SBH PercentofScores Direct Maternal
  • 15. CSU 2006 – Breeding and Genetics Seminar (17) Cole 200 6 Distribution of ReliabilitiesDistribution of Reliabilities 0 5 10 15 20 25 30 35 40 45 50 41-45 46-50 51-55 56-60 61-65 66-70 71-75 76-80 81-85 86-90 91-95 96-99 Reliability Percentage Direct Maternal
  • 16. CSU 2006 – Breeding and Genetics Seminar (18) Cole 200 6 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
  • 17. CSU 2006 – Breeding and Genetics Seminar (19) Cole 200 6 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
  • 18. CSU 2006 – Breeding and Genetics Seminar (20) Cole 200 6 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
  • 19. CSU 2006 – Breeding and Genetics Seminar (21) Cole 200 6 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
  • 20. CSU 2006 – Breeding and Genetics Seminar (22) Cole 200 6 SamplingSampling  Six datasets ofSix datasets of ~250,000~250,000 records each wererecords each were created by randomly sampling herd codescreated by randomly sampling herd codes without replacementwithout replacement  Datasets ranged fromDatasets ranged from 239,192239,192 toto 286,794286,794 observations, and all averagedobservations, and all averaged 7%7% stillbirthsstillbirths  A common pedigree file was used to facilitateA common pedigree file was used to facilitate comparisons between sire and MGS solutionscomparisons between sire and MGS solutions
  • 21. CSU 2006 – Breeding and Genetics Seminar (23) Cole 200 6 Bayesian (co)variance componentsBayesian (co)variance components estimatesestimates Var(Sire) Var(MGS) Cov(S-MGS) Sample Mean SD Mean SD Mean SD 1 0.010 0.002 0.018 0.002 0.004 0.001 2 0.007 0.002 0.017 0.002 0.005 0.001 3 0.009 0.001 0.019 0.002 0.005 0.001 4 0.008 0.001 0.019 0.002 0.004 0.001 5 0.008 0.001 0.018 0.002 0.002 0.001 6 0.009 0.002 0.017 0.002 0.004 0.001 Mean 0.009 0.002 0.018 0.002 0.004 0.001
  • 22. CSU 2006 – Breeding and Genetics Seminar (24) Cole 200 6 HeritabilitiesHeritabilities  Calving Ease (Direct) 8.6%  Calving Ease (MGS) 3.6%  Stillbirth (Direct) 3.0%  Stillbirth (MGS) 6.5%
  • 23. CSU 2006 – Breeding and Genetics Seminar (25) Cole 200 6 Genetic Correlations Among SB and CEGenetic Correlations Among SB and CE Trait CE SB Direct Maternal Direct Maternal CE Direct 1.00 0.46 0.67 0.25 Maternal 1.00 0.29 0.63 SB Direct 1.00 0.28 Maternal 1.00
  • 24. CSU 2006 – Breeding and Genetics Seminar (26) Cole 200 6 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 ($1800)
  • 25. CSU 2006 – Breeding and Genetics Seminar (27) Cole 200 6 Calving Ability IndexCalving Ability Index  CA$ 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
  • 26. CSU 2006 – Breeding and Genetics Seminar (28) Cole 200 6 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
  • 27. CSU 2006 – Breeding and Genetics Seminar (29) Cole 200 6 Calving Ease Genetic CorrelationsCalving Ease Genetic Correlations 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
  • 28. CSU 2006 – Breeding and Genetics Seminar (30) Cole 200 6 Stillbirth Genetic CorrelationsStillbirth Genetic Correlations 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
  • 29. CSU 2006 – Breeding and Genetics Seminar (31) Cole 200 6 Brown Swiss Calving EaseBrown Swiss Calving Ease Service sire correlations above diagonal, daughter belowService sire correlations above diagonal, daughter below Ctry CHE DEU NLD USA CHE .83 .81 .68 DEU .61 .77 .67 NLD .89 .76 .79 USA .70 .61 .76
  • 30. CSU 2006 – Breeding and Genetics Seminar (32) Cole 200 6 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
  • 31. CSU 2006 – Breeding and Genetics Seminar (33) Cole 200 6 Recent Calving Ease ResearchRecent Calving Ease Research
  • 32. CSU 2006 – Breeding and Genetics Seminar (34) Cole 200 6 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
  • 33. CSU 2006 – Breeding and Genetics Seminar (35) Cole 200 6 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 ScorebyHerd(%) Parity 1 Parity 2 0 20 40 60 80 100 1 2 3 4 5 Calving Ease Scores - Herd 2 ScorebyHerd(%)
  • 34. CSU 2006 – Breeding and Genetics Seminar (36) Cole 200 6 Test Edits -Test Edits - χχ22 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
  • 35. CSU 2006 – Breeding and Genetics Seminar (37) Cole 200 6 Percentage of Score by Parity In AllPercentage of Score by Parity In All (AN) and GoF Excluded (AG) Herds(AN) and GoF Excluded (AG) Herds 0 10 20 30 40 50 60 70 80 90 100 1 2 3 4 5 Calving Ease Score CountsbyHerd-Parity(%) Parity 1 - AN Parity 2 - AN Parity 1 - AG Parity 2 - AG
  • 36. CSU 2006 – Breeding and Genetics Seminar (38) Cole 200 6 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)
  • 37. CSU 2006 – Breeding and Genetics Seminar (39) Cole 200 6 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
  • 38. CSU 2006 – Breeding and Genetics Seminar (40) Cole 200 6 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
  • 39. CSU 2006 – Breeding and Genetics Seminar (41) Cole 200 6 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)
  • 40. CSU 2006 – Breeding and Genetics Seminar (42) Cole 200 6 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
  • 41. CSU 2006 – Breeding and Genetics Seminar (43) Cole 200 6 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