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Advancements in Genomic Evaluation Methods Explored

Discover the latest in genomic evaluation methods globally, including reliability, conversions for bulls, reduction in trait heritability, and low-cost genotyping. Explore genomic MACE, genotype exchange options, and international evaluation updates.

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Advancements in Genomic Evaluation Methods Explored

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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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