Benefits from cooperation in genomics
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Benefits from Cooperation in Genomics. Topics. Genomic cooperation Simulation of very large population Proposals for genotype sharing Country border issues and North American experience Genomic MACE equations USA update Actual HOL, JER, and BSW results Database and implementation.

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Presentation Transcript

Topics
Topics

  • Genomic cooperation

    • Simulation of very large population

    • Proposals for genotype sharing

    • Country border issues and North American experience

    • Genomic MACE equations

  • USA update

    • Actual HOL, JER, and BSW results

    • Database and implementation


Cooperative international projects
Cooperative International Projects

  • 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?



Human dna data sharing
Human DNA Data Sharing

"The highest priority of the International

Human Genome Sequencing Consortium

is ensuring that sequencing data from the

human genome is available to the world's

scientists rapidly, freely and without restriction."

National Human Genome Research Institute,

2008

"The principle of rapid pre-publication release

should apply to other types of data from other

large-scale production centers."

Wellcome Trust, 2003


Simulation results world holstein population
Simulation ResultsWorld Holstein Population

  • 40,360 older bulls to predict 9,850 younger 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


Genotype exchange options
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?


Problems of not sharing
Problems of Not Sharing

  • Genetic progress not as fast as with full access to genotypes

  • Severe limits on researcher access to genotypes (secrecy)

  • Genomics may lead to natural monopoly, similar to railroads

    • Small companies / countries can’t afford to buy sufficient genotypes


Share young bull cow genotypes
Share Young Bull, Cow Genotypes?

  • 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


North american cooperation
North American Cooperation

  • 174 markers, 1068 USA and CAN bulls

    • Illinois, Israel, and USDA researchers

    • 1991-1999

  • 367 markers, 1415 USA and CAN bulls

    • USDA, Illinois, and Israel

    • 1995-2004

  • 38,416 markers, 19,464 animals

    • USDA, Missouri, Canada, and Illumina

    • Oct 2007- Dec 2008


Country borders
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)


Foreign dna in north american data proven bulls young bulls and females
Foreign DNA in North American DataProven bulls, Young bulls, and Females


Usa update
USA Update

  • Genomic PTAs official in January

    • Traditional PTAs sent to Interbull

    • MACE used if foreign dtrs included

    • Genomic info used for most bulls

    • Genomic PTA transferred to descendants (to ancestors in future)

  • Jersey results also are official

  • More Brown Swiss needed (CHE)


Genomic methods
Genomic Methods

  • Direct genomic evaluation

    • Sum of effects for 38,416 genetic markers

    • Not published

  • Combined genomic evaluation

    • Include phenotypes of non-genotyped ancestors by selection index

  • Transferred genomic evaluation

    • Propagate info from genotyped animals to non-genotyped relatives by selection index


Genotyped animals n 19 464 as of december 2008
Genotyped Animals (n=19,464)As of December 2008


Experimental design update holstein jersey and brown swiss breeds
Experimental Design - UpdateHolstein, Jersey, and Brown Swiss breeds

Data from 2004 used to predict independent data from 2009


Reliability gain 1 by breed yield traits and nm of young bulls
Reliability Gain1 by BreedYield traits and NM$ of young bulls

1Gain above parent average reliability ~35%


Reliability gain by breed health and type traits of young bulls
Reliability Gain by BreedHealth and type traits of young bulls


Value of genotyping more animals actual and predicted gains for 27 traits and for net merit
Value of Genotyping More AnimalsActual and predicted gains for 27 traits and for Net Merit

Cows:

947

1916


Genomic mace genomics task force pete sullivan
Genomic MACEGenomics Task Force, Pete Sullivan

  • 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


Conclusions
Conclusions

  • Reliability for young animals

    • 30-38% for traditional parent averages

    • 60-70% genomic REL for USA HOL traits

    • 81% using 40,360 simulated bulls

    • 83% using 100K instead of 50K markers

  • High reliability requires large numbers of genotyped animals

    • Gains much smaller for USA JER and BSW breeds

  • Trading, sharing, profit is needed

  • Revised MACE may include genomics


Acknowledgments
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 and Jersey breed associations

    • Contributors to Cooperative Dairy DNA Repository (CDDR)


Cddr contributors
CDDR Contributors

  • National Association of Animal Breeders (NAAB, Columbia, MO)

    • ABS Global (DeForest, WI)

    • Accelerated Genetics (Baraboo, WI)

    • Alta (Balzac, AB, Canada)

    • Genex (Shawano, WI)

    • New Generation Genetics (Fort Atkinson, WI)

    • Select Sires (Plain City, OH)

    • Semex Alliance (Guelph, ON, Canada)

    • Taurus-Service (Mehoopany, PA)


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