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National and International Genomic Evaluation Methods

National and International Genomic Evaluation Methods. Topics. Evaluation schedules, data, reliability International genomic evaluation Conversions for young bulls Genomic MACE for old bulls Interbull Brown Swiss genomic proposal

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National and International Genomic Evaluation Methods

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  1. National and International Genomic Evaluation Methods

  2. Topics • Evaluation schedules, data, reliability • International genomic evaluation • Conversions for young bulls • Genomic MACE for old bulls • Interbull Brown Swiss genomic proposal • Reduction of yield trait heritability to reduce elite cow PTA, young bull PA bias • Low density, low cost genotyping

  3. Traditional, Genomic, MACE Schedule • Review of Dec/Jan, Feb, and Apr evaluations • Recompute genomic PTAs after new MACE PTAs arrive • Aug evaluation must start earlier to provide genomic PTAs of young bulls to Interbull • Interbull conversions to begin in Aug, MACE for proven bulls in 2010 • Genotype, cow PTA, pedigree exchange with Canada, Switzerland, etc.

  4. Genomic Methods • Direct genomic value (DGV) • Sum of effects for 38,416 genetic markers • Now displayed for NM$ with chromosome query • Combined genomic evaluation • Include phenotypes of non-genotyped ancestors • Selection index includes 3 PTAs per animal • Traditional, direct genomic, and subset PTA • Transferred genomic evaluation (code 2) • Propagate from genotyped animals to non-genotyped descendants by selection index • Propagation to ancestors being developed

  5. January Evaluation • HO, JE genomic PTAs official in Jan. • Genomic from Dec 1, domestic Dec 18 • Traditional PTAs sent to Interbull • MACE used if foreign daughters included • Genomic PTA used for most bulls (80%) • Traditional used if many new daughters • Genomic PTA transferred to descendants (to ancestors in future)

  6. February Evaluation • Interim, official only for new genotypes • Animals genotyped during Dec and Jan • Active bulls not updated officially • Unofficial PTAs provided in March for proven bulls • March evaluation (interim interim) • Added 96 bulls accidentally left out of Feb • Tested fast reliability approximation • Brown Swiss now have 719 genotyped • Traded with Switzerland in March 2009

  7. April Evaluation • Compute domestic, then genomic • January type used by mistake • Reliability approximate, not exact • Selection index calculation • Replace previous with current MACE • SNP effects and subset PTA same • Similar to young bull calving ease • Suggested by CDN researchers

  8. June Evaluation (Plans) • Net Merit as sum instead of trait • Evaluate traits, then sum, instead of sum traits, then evaluate NM as trait • Large differences for CAN cows • Individual traits were converted to US scale, but not NM • Small changes for bulls and US cows • Nearly all changes < $50 • Corr (NM as sum, NM as trait) > .996

  9. August Evaluation (Plans) • Interbull converts genomic PTAs • Young bulls only • EU requires 50% REL for marketing • Proven bulls next year (2010) • AIPL must compute domestic and genomic earlier to meet deadline • Decrease yield heritability to make PAs and cow PTAs less biased

  10. Genomic MACEInterbull Genomics Task Force • Residuals correlated across countries • Repeated tests of the same major gene, or • SNP effects estimated from common bulls • Let cij = proportion of common bulls • Let gi = DEgen / (DEdau + DEgen) • Corr(ei, ej) = cij * Corr(ai, aj) * √(gi * gj) • Avoids double counting genomic information from multiple countries i, j • New deregression formulas needed

  11. Worldwide Dairy Genotypingas of January 2009 1Using a customized Illumina 50K chip (different markers)

  12. Foreign DNA in North American DataProven bulls, Young bulls, and Females

  13. Country Borders • Most phenotypic data collected and stored within country • Genomic data allows simple, accurate prediction across borders • Need traditional EBV or PA for foreign animals, but not available for young bulls, cows, or heifers • May need full foreign pedigrees • Genomic evaluations official on USA scale for many foreign animals (not just CAN)

  14. International Evaluation • Traditional genetic evaluations • MACE instead of merging phenotypes • Small benefits expected from data merger • Proven bulls only, not cows or young bulls • Parentage testing, genetic recessives, pedigrees done by breed associations • Genomics: what role for Interbull? • Benefits of sharing genotypes are large • Brown Swiss genotype sharing proposal

  15. Genotype Exchange Options • Give away for free (not likely) • Genotype own bulls, then trade? • Trade an equal number or all bulls? • Country A has 5000 and B has 1000 • Proportional to population size? • Trade among organization pairs or create central genomic database? • Service fee for young animals to pay for ancestor genotyping?

  16. Share Young Bull, Cow Genotypes?USA – CAN exchange • May be marketed in >1 country • Exchange of young animals and females more important as their REL increases with genomics • Helps to synchronize databases • Could lead to joint evaluation

  17. Problems of Not Sharing • Genetic progress not as fast as with full access to genotypes • Limits on research access to genotypes (secrecy) • Genomics may lead to natural monopoly • Small companies / countries can’t afford to buy sufficient genotypes

  18. Simulation ResultsWorld Holstein Population • 40,360 older bulls to predict 9,850younger bulls in Interbull file • 50,000 or 100,000 SNP; 5,000 QTL • Reliability vs. parent average REL • Genomic REL = corr2 (EBV, true BV) • 81% vs 30% observed using 50K • 83% vs 30% observed using 100K

  19. Genotyped Animals (n=25,393)In North America as of April 2009

  20. Experimental Design - UpdateHolstein, Jersey, and Brown Swiss breeds Data from 2004 used to predict independent data from 2009

  21. Reliability Gain1 by BreedYield traits and NM$ of young bulls 1Gain above parent average reliability ~35%

  22. Reliability Gain by BreedHealth and type traits of young bulls

  23. Genomic Daughter Equivalentsfrom April 2009 published reliabilities

  24. Expected Change in Net MeritHolstein – April 2009 • SD = 163 * √(RELG – RELT ) • = $95 for young bulls (.69 - .35) • = $23 for proven bulls (.86 - .84) • Daughter equivalents for NM$ • 10 from parent average • 30 from genomics • 40 total for young animals

  25. Value of Genotyping More AnimalsActual and predicted gains for 27 traits and for Net Merit Cows: 947 2711

  26. Do Cows and Old Bulls Help?Research by Marcos da Silva, BFGL, using Nov 2004 cutoff

  27. Yield Trait Heritability • 30% used Aug 1997-present for HO • 35% used Nov 2000-present for JE and BS • Van Tassell et al., 1999 JDS 82:2231 • Deviations limited to 4 SD since 1997 • Herd variance adjustment since 1991 • 25% from 1989-1997 • 20% from 1974-1988 • 19% from 1966-1973 • 31% from 1962-1965

  28. Heritability Test • Change in PTA protein of elite cows and bulls • Top 100 cows in each breed • Top 10 bulls in each breed • Predict son’s current DYD from dam’s 2005 PTA • 30% h2 for HO, GU, AY; 35% JE, BS • 25% h2 for HO, GU, AY; 29% JE, BS • 20% h2 for HO, GU, AY; 23% JE, BS • 15% h2 for HO, GU, AY; 18% JE, BS

  29. Effect of h2 on Top PTAs for ProteinChange in cow and bull means compared to current h2 1JE and BS heritability set to HO h2 * (.35 / 30)

  30. Effect of h2 on Corr(dam, son)Dam PTA 2005 and son DYD protein 2009 1JE and BS heritability set to HO h2 * (.35 / 30)

  31. Low Density SNP Chip • Choose 384 marker subset • SNP that best predict net merit • Parentage markers to be shared • Use for initial screening of cows • 40% benefit of full set for 10% cost • Could get larger benefits using haplotyping (Habier et al., 2008)

  32. Marker Effects for Net Merit

  33. Gains by Trait for 384 SNPsselected for Holstein Net Merit

  34. Conclusions • Genomic reliability > traditional • 30-40% with traditional parent average • 60-70% using 8,100 genotyped Holsteins • 81-83% from 40,000 simulated bulls • Gains for US Jersey and Brown Swiss breeds smaller, but improving • Young bull conversions, reduced yield heritability in May Interbull test • Due April 28

  35. Acknowledgments • Genotyping and DNA extraction: • USDA Bovine Functional Genomics Lab, U. Missouri, U. Alberta, GeneSeek, Genetics & IVF Institute, Genetic Visions, and Illumina • Computing: • AIPL staff (Mel Tooker, Leigh Walton, Jay Megonigal) • Funding: • National Research Initiative grants • 2006-35205-16888, 2006-35205-16701 • Agriculture Research Service • Holstein, Jersey & Brown Swiss breed associations • Contributors to Cooperative Dairy DNA Repository (CDDR)

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