Implementing and improving genomic evaluations

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Implementing and improving genomic evaluations
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Genomic evaluation procedure

• Nominate animals for genotyping
• Collect blood, hair, ear tissue, or semen
• Extract DNA and genotype
• Assign genotypes from image files
• Check genotypes for call rate, parent-progeny
  consistency, and X homozygosity for bulls
• Collect parent averages/estimated breeding values
  (EBV)
• Calculate evaluations
• Distribute evaluations to requesters

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Nominate animals

• Participating artificial-insemination (AI)
  organizations have 5-year exclusive rights to
  evaluate bulls genomically
• Each AI organization genotypes its first-choice
  flushes, which usually avoids duplicate genotypes
• Web-based system being developed to collect
  nominations
• Avoid duplication
• Confirm validity of identification (ID) and
  pedigree
• Breed associations developing cow genotyping
  service

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DNA sources

• Semen from Cooperative Dairy DNA Repository
  primary source of historical DNA
• Cow genotypes primarily from associated research
  projects
• Blood and hair the most common sources of DNA for
  calves and cows
• Bulls in waiting genotyped from semen
• Ear tissue being evaluated but has not been used
• Some DNA from samples collected for parentage
  testing

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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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Assign genotypes

• Each laboratory sends image files to BFGL
• Methods developed to achieve consistent and high
  call rates
• Direct reporting of genotypes to AIPL planned for
  December 2008

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Check genotypes

• 90 call rate required
• Each parent-progeny pair checked for conflicting
  homozygotes
• Maternal grandsire (MGS) also checked with higher
  threshold of conflicts
• Cases with many conflicts or no parent genotyped
  checked against all genotyped animals for
  possible parent
• Heterozygous SNP on X counted
• (none expected for bulls)

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Collect parent averages/EBV

• Combined U.S.-Canadian analysis requires
  comparable evaluations for all animals
• Interbull evaluations used for bulls
• Canadian Dairy Network provides evaluations of
  Canadian genotyped cows and maternal ancestors of
  genotyped animals
• Holstein USA provides type evaluations
• Previous Interbull evaluations used at
  traditional triannual evaluation releases

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Reliability of evaluations

• Reliability from inverse of a matrix with order
  the number of genotyped animals
• Approximation necessary as number of genotyped
  animals increases
• Daughter equivalents discounted by 0.6 to
  represent better the reliability of 2003 data in
  predicting bulls first evaluated in 2008

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Accurate genomic evaluations

• Estimates of SNP effects required
• Evaluations with high reliability provide the
  most information
• Recent animals more useful than ones from earlier
  generations
• Reliability of genomic evaluations increases with
  number of predictor animals

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Genotyped animals (October 2008)
Breed Bulls Cows Predictors
Holstein 12,275 2,445 7,821
Jersey 1,205 369 1,428
Brown Swiss 365 3 359
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Schedule

• Calculate SNP effects with each of 3 annual
  traditional evaluations
• Calculate genomic evaluations once or more
  between traditional evaluations, monthly?
• Recalculate SNP effects if significant number of
  predictor animals added
• Use existing SNP effects if only young animals
  added

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Official release in 2009

• Added information from genomic evaluations
  propagated to evaluations of descendents without
  genotypes
• National Association of Animal Breeders (NAAB) to
  manage bull-owner notification and sharing among
  AI organizations
• Public release of genomic evaluations
• Cows soon after calculated
• Bulls when enrolled with NAAB or Canadian AI
  organization
• Shared by agreement with owner

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Improvements

• Employ bar codes on sample containers to reduce
  errors and improve lab efficiency
• Widely used
• Rely on breed associations to resolve
  parent-progeny genotype conflicts
• Will happen, especially if parentage verification
  is switched from microsatellites to SNP
• Enroll animals that might be genotyped at birth
  to avoid ID issues when genotyped
• Needs to be required low cost enrollment
  available

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Plans to increase accuracy

• Genotype more predictor bulls
• Reach 1,500 Brown Swiss through foreign
  collaboration?
• Increase genotyped Jerseys from both domestic
  animals and possible foreign collaboration
• Investigate across-breed analysis to allow data
  from Holsteins to improve accuracy for Jerseys
  and Brown Swiss

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Implications

• Extraordinarily rapid implementation of genomic
  evaluations
• Young bull acquisition and marketing as well as
  cow selection now based on genomic evaluations
• Industry groups taking responsibility for
  genotyping 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