Genetic evaluation using combined data from all breeds and crossbred cows

1. Genetic evaluation using combined data from all breeds and crossbred cows

2. Jersey  Holstein USDA Yearbook of Agriculture 1947 From USDA research herd at Beltsville, MD

3. Red Dane  Jersey USDA Yearbook of Agriculture 1947 Crossbreds averaged 12,904 pounds of milk and 588 pounds of butterfat, outperforming dams by more than sire proof predictions (Fohrman,1947). Advanced register Holsteins averaged 13,833 pounds of milk and 493 pounds of fat in 1945.

4. Goals • Evaluate crossbred animals without biasing purebred evaluations • Accurately estimate breed differences • Compare crossbreeding strategies • Compute national evaluations and examine changes • Display results without confusion

5. All-Breed Analyses • Crossbred animals • Will have PTAs, only 3% did before if in breed association grading-up programs • Reliable PTAs from both parents • Purebred animals • Information from crossbred relatives • More herdmates (other breeds, crossbreds) • Routinely used in other populations • New Zealand (1994), Netherlands (1997) • USA goats (1989), calving ease (2005)

6. Methods • All-breed animal model • Purebreds and crossbreds together • Relationship matrix among all • Unknown parents grouped by breed • Variance adjustments by breed • Age adjust to 36 months, not mature • Within-breed-of-sire model examined but not used

7. Data • Numbers of cows of all breeds • 22.6 million for milk and fat • 16.1 million for protein • 22.5 million for productive life • 19.9 million for daughter pregnancy rate • 10.5 million for somatic cell score • Type traits are still collected and evaluated in separate breed files

8. Purebred and Crossbred DataUSA milk yield records

9. Crossbred Cowswith 1st parity records

10. Number of Cows with Records(with > 50% heterosis; March 2007)

11. Number of Cows with Records(with > 50% heterosis; March 2007)

12. Crossbred Daughters Addedfor sires in top 10 NM$ within breed

13. Heterosis for Yield TraitsPercent of Parent Breed Average

14. Breed Effects and Heterosis • Three estimates of breed differences: • From phenotypic breed differences • From herds containing crossbred cows • From all-breed model using all data • All three estimates were similar • Estimates of general heterosis from 2001 and 2003 studies were used in the current research and not re-estimated

15. Unknown Parent Groups • Look up PTAs of known parents • Estimate averages for unknowns • Group unknown parents by • Birth year • Breed • Path (dams of cows, sires of cows, parents of bulls) • Origin (domestic vs other countries)

16. All- vs Within-Breed EvaluationsCorrelations of PTA Milk

17. Display of PTAs • Genetic base • Convert all-breed base to within-breed bases (or vice versa) • PTAbrd = (PTAall – meanbrd) SDbrd/SDHO • PTAall = PTAbrd (SDHO/SDbrd) + meanbrd • Heterosis and inbreeding • Both effects removed in the animal model • Heterosis added to crossbred animal PTA • Expected Future Inbreeding (EFI) and merit differ with mate breed

18. Milk (kg)Genetic trend on all-breed base

19. Fat (kg)Genetic trend on all-breed base

20. Protein (kg)Genetic trend on all-breed base

21. Somatic Cell ScoreGenetic trend on all-breed base

22. Productive LifeGenetic trend on all-breed base

23. Daughter Pregnancy RateGenetic trend on all-breed base

24. EBV differences from Holstein estimated from an all-breed model

25. Phenotypic breed differences from Holstein from an all-breed model

26. EBV differences from Holstein estimated from an all-breed model

27. Phenotypic breed differences from Holstein from an all-breed model

28. Net Merit Relative EmphasisIn cooperation with Dr. Tony Seykora et al. DPR = daughter pregnancy rate (fertility), CA$ is index of calving ease and stillbirth

29. NM$, FM$, CM$ Economic Values Other values are same in each index: PL 29, SCS -150, Size -14, Udder 28, F&L 13, DPR 21, CA$ 1

30. Other Trait Estimates • Calving ease and stillbirth estimated from breed means • 7.3 million HO, 37000 JE, 17000 BS, 2000 GU, 2000 AY, 300 MS • Body size composite estimated from mature weight • Udder composite, Feet / Leg composite extrapolated from regressions on other traits within Holsteins • Size, PL, milk, DPR, SCS

31. Correlations used in Predictions Canada now scores linear conformation traits of all breeds on the same scale

32. Assumed Effects – Other TraitsTransmitting ability differences from Holstein

33. Merit of F1 Holstein Crossbreds Compared to 2005 genetic base for Holstein

34. Later Generation Crosses Compared to 2005 genetic base for Holstein

35. Three-Breed Crosses USDA Yearbook of Agriculture 1947 Butterfat yield of three breed crosses was greater than from their F1 crossbred dams. Three breed crosses averaged 14,927 pounds of milk and 641 pounds of butterfat as 2-year-olds in 1947.

36. Scandinavian and French Breeds • AIPL has pedigree records for other breeds (NR, SR, MO); but few production records yet • For further information: • Interbull conversions to Ayrshire base • U. Minnesota scientists (Heins et al.)

37. Conclusions

38. Conclusions (1) • All-breed model accounts for: • Breed effects and general heterosis • Unequal variances within breed • May 2007 implementation expected • PTA converted back to within-breed bases, crossbreds to breed of sire • PTA changes larger in breeds with fewer animals

39. Conclusions (2) • Breed effects were estimated • Yield, PL, SCS, DPR by all-breed model • Calving ease and stillbirth breed means • Udder, F&L composites from other traits • Lifetime Net Merit formula for August 2006 applied • Holsteins still superior for FM$

40. Conclusions (3) • BS x HO and JE x HO crosses had higher NM$ and CM$ than HO • BS x JE had higher CM$ than HO • Three-breed crosses (HO, BS, JE) are higher than HO backcrosses for CM$, similar for NM$ • Use best bulls within each breed

41. Acknowledgments • Several others at AIPL contributed greatly to this project, including Mel Tooker, George Wiggans, John Cole, Jay Megonigal, and Ashley Sanders