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Inbreeding Adjustments and Effect on Genetic Trend Estimates

Inbreeding Adjustments and Effect on Genetic Trend Estimates. Adjustments Introduced Feb 2005. Inbreeding depression: Remove by regression in animal model Then include expected future inbreeding EFI = .5 mean relationship to current cows Parity variance Heterogeneous variance refinement

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Inbreeding Adjustments and Effect on Genetic Trend Estimates

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  1. Inbreeding Adjustments and Effect on Genetic Trend Estimates

  2. Adjustments Introduced Feb 2005 • Inbreeding depression: • Remove by regression in animal model • Then include expected future inbreeding • EFI = .5 mean relationship to current cows • Parity variance • Heterogeneous variance refinement • September 2004 test run included both

  3. Inbreeding AdjustmentsVanRaden and Smith 1999 JDS 82:2771 • Subtract regression (b) from y • YD0 = y - m - p - c - b (Fcow) • DYD0 and PTA0 reflect 0 inbreeding • Add expected future inbreeding • PTAEFI = PTA0 + b (EFI - EFIbase) • PAEFI = PA0 + b (EFI - EFIbase) • DYDEFI = DYD0 + b (EFI - EFIbase)

  4. Effects of Inbreeding Adjustment • Genetic evaluations of recent Holsteins • Corr (PTA, PTAEFI) = .998 for bulls • Corr (PTA, PTAEFI) = .993 for cows • Genetic correlations of USA with other countries declined by .01 (Sep 1999 test run) • Genetic trend • Yield trends were 6% lower for PTAEFI • Fertility, longevity trends 14-25% lower

  5. Changes in Trends and Trend Testsfrom Inbreeding Adjustments

  6. Parity Variance Adjustments • Trend test 1 was .014 (fail), now .008 (pass) for Jerseys. Holsteins were OK. • Deviations for yield are multiplied by [1.07 1.00 .95 .90 .85] (parities 1-5) • Genetic trend for protein decreased by .004 genetic SD / year (2% change) • Corr (official, adjusted PTA) = .9998 for recent Holstein bulls

  7. USA vs Non-USA Bull TrendsBefore (Aug) and After (Sep) Adjustments

  8. Effect on Top 100 Bulls • Average number of USA bulls in top 100 across all 27 protein scales • Increase from 24.5 to 25.3 (Holstein) • Increase from 53.8 to 56.3 (Jersey) • USA genetic trend • Decreased 6% (Holstein) • Decreased 9% (Jersey)

  9. Conclusions • Boichard et al (1995) stated that biased genetic trend “strongly disturbs international germplasm exchanges based on conversion formulas...” • MACE is robust to trend bias • Trend tests should not be required

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