1. Multi-breed Evaluation J. Keith Bertrand University of Georgia, Athens

2. Multi-Breed Evaluation (MBE) Analyzing the data from animals of any breed composition and providing genetic values (EPDs) for virtually all animals in the data base, regardless of breed composition.

3. Why Consider Multi-Breed Genetic Evaluation? Genetic values can be computed on animals of any breed composition contained in the data base or population. There is a potential increase in the accuracy of the genetic values due to the inclusion of additional information. Also, there is an opportunity to provide genetic values and services to new clients.

4. Effects in Model for Genetic Evaluation of Purebred Data Maternal Permanent Environmental Effect Direct Genetic Effect + Maternal Genetic Effect + Model : WWT = Fixed Effects + Genetic value (EPD) provided by for an animal = Estimated Genetic Effects

5. Effects in MBE Model Maternal Permanent Environmental Effect Direct Genetic Effect + Maternal Genetic Effect + Direct Breed Effect + Maternal Breed Effect + Direct Heterosis + Maternal Heterosis + Multi-breed Model : WWT = Fixed Effects + Genetic value provided by MBE for an animal = Est. Breed Effects + Est. Genetic Effects

6. Estimation of Heterosis and Breed Effects in MBE Model Typical system of Equations: Cb = y Application of Bayesian Methodology: (C + V p -1 )b = y + V p -1  p If V p is very large = data determines estimate If V p is very small = prior (literature) determines estimate

7. Heterosis Heterosis is the increased performance of crossbred animals due to pairing of alleles that originate from different breeds Heterosis affects the phenotypic performance of individuals and needs to be taken into inconsideration in the prediction of EPDs

8. Estimation of Heterosis Breeds are grouped into biological types for heterosis computations: British [B], Continental [C], Zebu [Z], Other [O] 10 comb.: BxB, BxC, BxZ, BxO, CxC, CxZ, CxO, ZxZ, ZxO, OxO Why Group? – With 60 or more breeds represented, more than seventeen hundred or more possible F 1 combinations are possible

9. Estimating Heterosis as the Fraction of F 1 Heterosis Contibuted by Different Breed Combinations 1/16 h BB 1/16 h BZ 1/8 h BC ¼ Hereford [B] 1/8 h BC ¼ Angus [B] 1/16 h BZ 1/8 h CZ ¼ Brahman [Z] 1/8 h BC ½ Gelbvieh [C] ¼ Angus [B]½ Gelbvieh [C] Sire Dam h ij = F 1 heterosis estimate for the i and j breed comb. Heterosis Est. = 1/16 h BB + 3/8 h BC + 1/8 h BZ + 1/8 h CZ

10. Accounting For Breed Composition Animal pedigrees are traced back as far as possible. The breed combinations of these “founder” animals are determined. These founder animals may not be representative of their breed(s). All the genes in the animal originated from these founders.

11. Breed of Founder (BOF) Effects Some breeds are fit in model: Angus, Brahman, Charolais, Gelbvieh, Hereford, Limousin, Simmental, etc. Some breeds are placed into groups due to small numbers of observations. Simmental Evaluation: American, British, Continental, Dairy, and Mixed Gelbvieh Evaluation: British Beef, British Dairy, Continental Beef, Continental Dairy, and Zebu.

12. Breed of Founder (BOF) Effects BOF fit in model to account for the genes from various breeds that are contributed by the founder animals. Yearly or generational BOF effects are fit in model to account for genetic trend in the animals of different breeds that enter the population over time. Animal: ½ Simmental, ¼ Angus, ¼ Brahman BOF effect = ½ BOF SIML + ¼ BOF ANG + ¼ BOF BRA (BOF effects est. using a combination of data and literature values.)

13. Breed of Founder by Generation Group Solutions from Gelbvieh MBE Generation Group British Beef GelbviehAngusLimousin < 19806.446.50.024.7 1981-198511.747.87.724.7 1986-199013.649.814.324.5 1991-199512.650.715.224.0 1996-200210.451.414.123.8 Prior-7.958.40.025.6

14. Weaning Weight EPD Gametic Trends for Angus and Limousin Animals from AGA MBE

15. Multi-Breed Evaluation (MBE) MBE applied to a single breed association data set is not meant to provide information on “true breed differences”.

16. Weaning Weight EPD Trends for Angus and Limousin Animals from Limousin (NALF) and Gelbvieh (AGA) Evaluations

17. Incorporation of Outside EPDs Into MBE Evaluation Significant numbers of sires from another breed may be present in the data set. Similar to the evaluation of heterosis and BOF effects, the data and the outside EPD can be combined. The outside EPD information can be used to better evaluate and rank a set of bulls within a breed. This assumes no sire by breed-of- dam interactions. The base of external EPDs has no influence on the EPDs predicted in the MBE

18. Rank Correlation Between External EPDs and Gelbvieh MBE EPDs of Angus Sires When External Information is Ignored or Included AAA Accuracy External EPDs Ignored External EPDs Included No. of Sires 0.0 - 0.20.390.62192 0.2 - 0.40.260.75505 0.4 – 0.60.270.82299 0.6 - 0.80.330.91575 0.8 – 1.00.190.95258

19. Incorporation of Outside EPDs Into MBE: Magnitude of Outside vs MBE EPDs An Example: Two high accuracy Angus bulls with AAA weaning EPDs of 60 and 20 lbs may not have the same magnitude of EPD in the MBE for another breed. However, if the two bulls have very little data in the MBE, the difference in their EPDs out of the MBE will be close to 40 lbs.

20. Multi-Breed Evaluation (MBE) Does MBE provide EPDs? People expect sire EPDs to predict the difference in the expected average performance between the progeny of two sires provided they were mated to dams of the same genetics, including breed type. Sire A EPD = 30 lbs, Sire B EPD = -5 lbs Expected difference in the average performance of future progeny produced by two sires = 30 – (-5)) = 35 lbs

21. Does MBE provide EPDs? Sire A: 1/2 Limousin, 1/2 Brahman Sire B: 100% Limousin Bred to genetically similar Limousin dams EPD A - EPD B = provides a prediction of the difference in the additive transmitting abilities between sires A and B. Average perf. of prog A - average perf. of prog B = TA A - TA B + (1/2 F1 het CZ )

22. What’s Next For MBE

23. Prototype Multi-Breed Evaluation (MBE) Several breeds have proposed the pooling of their data sets for a prototype MBE for growth traits. Breed associations will be responsible for creating the necessary cross-link identification of animals. Consortium will begin building the data base containing pedigrees from all breeds and assigning animal identification to use in MBE. Goal is to have an initial analysis completed sometime this summer in order to evaluate hardware and software requirements.

24. Inclusion of Records From Early Weaned Animals Records from animals outside of acceptable age ranges are eliminated (BIF recom- mendation for weaning weight: 160-250 days. Weaning weight records from early weaned animals eliminated due to age range edits. Consortium asked to solve the problem.

25. Implementation of Models For Longitudinal Data Growth traits could be considered as repeated or longitudinal measures across time on the same animal. Fitting models that account for the longitudinal nature of growth would allow for weight at any age to be included in the evaluation

26. Several Measures on the Same Animal Weight Age (days) 1 125 205 365 735

27. Partitioning of Animal Differences Using Using A Random Regression Model y jk =  0j +  1j (A) +  2j (A 2 ) +  3j (A 3 ) +  jk  ij =  i + a ij + p ij +m il +pe il +e ij y jk = (  0 + a 0j + p 0j +m 0l +pe 0l +e 0j ) + (  1 + a 1j + p 1j +m 1l +pe 1l +e 1j )(A) + (  2 + a 2j + p 2j +m 2l +pe 1l +e 2j )(A 2 ) + (  3 + a 3j + p 3j +m 3l +pe 3l +e 3j )(A 3 ) +  jk

28. Breeding Values (BV) Computed From Random Regression Models BV of animal j at age n = a 0j + a 1j (A n ) + a 2j (A n 2 ) + a 3j (A n 3 )

29. Hypothetical Weight EPDs From Random Regression Model Analysis Age 1 205 365 EPD

30. Summary MBE combines prior literature estimates and performance and pedigree information to provide EPDs for animals of various breed combinations. At the request of several breed associations, NBCEC will conduct a prototype MBE for growth traits on a pooled data set. NBCEC is conducting research to improve MBE.