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  • 8/3/2019 Foreign Collaborations 1

    1/22

    G.R. WiggansAnimal Improvement Programs Laboratory

    Agricultural Research Service, USDABeltsville, MD

    [email protected]

    2008G.R. WiggansDHI-Provo Herd Management Conference (1)

    Whats Coming in

    Genomic Evaluationsand How It Affects You

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    G.R. Wiggans 2008DHI-Provo Herd Management Conference (2)

    What are genomic evaluations?

    DNA extracted from blood, hair, or semen ~40,000 genetic markers (SNPs) evaluated

    For each SNP, difference in PTA between

    animals with one allele compared to theother is estimated

    Genomic evaluation combines SNP effect

    estimates with existing PA or PTA

    Genomic data contribute ~11 daughterequivalents to reliability

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    What is a SNP?

    Single-nucleotide polymorphism

    Place on the chromosome where animals differ in thenucleotides (A, C, T, or G) they have

    Usually not part of the gene that controls a trait quantitative trait locus (QTL)

    With enough SNPs, association between SNP alleles

    and QTL alleles gives useful evaluations

    SNPs chosen to be distributed evenly and have bothalleles well represented in population

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    Genomic vs. traditional PTA

    Genotype can be thought of as source of informationlike parents, progeny, and records

    Official PTA will have a indicator if they include agenomic contribution

    One genotype is used to calculate genomicevaluations for all 29 traits

    Genomic evaluations used the same way astraditional PTA

    Expected to increase rate of genetic improvementbecause of a large decrease in generation interval

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    Whats happened so far

    Illumina BovineSNP50 BeadChip developed

    Accuracy of genomic information assessed by using2003 evaluations of bulls born before 2000 to predict2008 evaluations of young bulls

    Test evaluations began to provide genomicevaluations of bull calves in April

    Jersey results released in October

    New results released every 2 months

    Nearly 15,000 animals genotyped through October

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    Genotyped animals (October 2008)

    Breed Bulls Cows PredictorsHolstein 12,275 2,445 7,821

    Jersey 1,205 369 1,428

    Brown Swiss 365 3 359

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    How to get animals genotyped

    Participating AI organizations have 5-year exclusiveright to evaluate bulls genomically

    Each AI organization genotypes first-choice flushes,thereby usually avoiding duplicate genotypes

    Web-based system being developed to collectnominations

    Avoid duplication

    Confirm validity of ID and pedigree

    Breed associations developing cow genotypingservice

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    What can go wrong

    Sample doesnt provide adequate DNA quality orquantity

    Genotype has many SNPs that cant be determined(90% call rate required)

    Genotype conflicts with parent(s)

    Pedigree error

    Sample ID error

    Laboratory error

    Genotype checked against all others to find trueparent

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    Collaboration with Canada

    Semex Supported since beginning of genomics

    research

    Contributed valuable genotypes to firstaccuracy test

    Genotypes will be shared between AIPL and

    Canadian Dairy Network

    AIPL and University of Guelph collaboration

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    Collaboration with Canada (cont.)

    Canadian and U.S. evaluations of genotypedanimals expected to have same accuracy becausesame set of predictor animals used

    Canada expects official release of genomicevaluations in April 2009

    Young animals expected to be evaluated only byone country

    Common procedures between 2 countries assistin industry acceptance

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    DNA laboratories

    Research

    Bovine Functional Genomics Laboratory (BFGL), USDA(Beltsville, MD)

    University of Alberta (Edmonton, AB, Canada)

    University of Missouri (Columbia, MO)

    Illumina (San Diego, CA)

    Commercial

    GeneSeek (Lincoln, NE)

    Genetics & IVF Institute (Fairfax, VA)

    Genetic Visions (Middleton, WI) DNA LandMarks (Saint-Jean-sur-Richelieu, QC, Canada)

    Maxxam Analytics (Mississauga, ON, Canada)

    ABS (DeForest, WI, through SyGen/PIC, Franklin, KY )

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    Use of genomic evaluations

    AI organizations determine which youngbulls to buy

    Considered in selection of mating sires

    Impact on bull dam selection will increase

    May be used to market semen from 2-year-old bulls

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    January 2009

    Genomic evaluations become official

    Genotyped ancestors contribute theirevaluations to descendents

    Evaluations of all genotyped females are public

    Evaluations of males enrolled with NAAB or24 months old are public

    Young-bull genomic evaluations may be sharedamong AI organizations or disclosed by owner

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    Impact on producers

    Young-bull evaluations will have accuracy of earlyfirst-crop evaluations

    AI organizations may market genomicallyevaluated 2-year-olds

    Genotypes for bull dams likely to be required

    Rate of genetic improvement likely to increase byup to 50%

    Progeny-test programs will change

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    Schedule

    Calculate SNP effects with each of 3 annualtraditional evaluations

    Calculate genomic evaluations once or more

    between traditional evaluations, monthly?

    Recalculate SNP effects if significantnumber of predictor animals added

    Use existing SNP effects if only younganimals added

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    Improvements

    Require bar codes on sample containers toreduce errors and improve lab efficiency

    Establish routine system to detect, report, andresolve parent-progeny genotype conflicts

    Enroll animals that might be genotyped at birthto minimize ID issues when genotyped

    Reduce processing time by enabling labs toreport genotypes directly to AIPL

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    Plans to increase accuracy

    Genotype more predictor bulls(most active bulls expected to be genotyped soon)

    Reach 1,500 Brown Swiss through foreigncollaboration?

    Increase genotyped Jerseys from both domesticanimals and possible foreign collaboration

    Investigate across-breed analysis to allow datafrom Holsteins to improve accuracy for Jerseysand Brown Swiss

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    International implications

    All major dairy countries investigating genomicselection

    Interbull meeting in January to discuss howgenomic evaluations should be integrated

    AI organizations need to find balance betweencompetitive benefits from treating genotypesas proprietary versus sharing

    Importing countries must change rules to allowfor genomically evaluated young bulls

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    Low-cost genotyping research

    Develop a genetic test thats cheap enough toenable use for most animals

    Provide parentage verification/discovery

    Provide genetic estimate useful for first-stagescreening

    384 SNPs proposed for first test

    High throughput procedures being developed

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    Longer-term possibilities

    Determine inheritance of individualchromosome segments (haplotyping)

    May allow better tracking of QTL

    Approximate genotypes of missing ancestorsto increase predictor population

    Increase number of SNPs or even use entireDNA sequence

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    Implications

    Extraordinarily rapid implementation ofgenomic evaluations

    Young bull acquisition and marketing

    now based on genomic evaluations

    Increase in diversity of bull dams

    considered

    Industry groups taking responsibility forgenotyping and validation

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    Financial support

    National Research Initiative grants, USDA

    NAAB (Columbia, MO) ABS Global (DeForest, WI) Accelerated Genetics (Baraboo, WI) Alta (Balzac, AB)

    Genex (Shawano, WI) New Generation Genetics (Fort Atkinson, WI) Select Sires (Plain City, OH) Semex Alliance (Guelph, ON) Taurus-Service (Mehoopany, PA)

    Holstein Association USA (Brattleboro, VT)

    American Jersey Cattle Association (Reynoldsburg, OH)

    Agricultural Research Service, USDA