Transition of genomic evaluation from a research project to a production system

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Transition of genomic evaluation from a research
project to a production system
Abstr. 278
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Genomic evaluation system

• Provides timely evaluations of young bulls for
  purchasing decisions
• Increases accuracy of evaluations of bull dams
• Assists in selection of service sires,
  particularly for low-reliability traits

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Obtaining genotypes

• Collect tissue sample (hair and blood most common
  for calves)
• Extract DNA
• Bind DNA to chip (12 samples/chip)
• Scan chip to create intensity files
• Call genotypes (GenomeStudio software)

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Before clustering adjustment
86 call rate
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After clustering adjustment
100 call rate
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Calling genotypes

• Genotypes called by Tad Sonstegard, BFGL, through
  April 2009
• AIPL staff trained to run GenomeStudio
• Cluster files shared with 4 commercial labs to
  promote call harmonization
• Labs began providing genotypes in June

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Managing sample ID

• Web query established for nominations
• Indicates missing pedigrees
• Designates who receives evaluation
• Provides sample status, including rejection
  reasons
• Query used by labs to convert sample ID to
  registration number and detect ID entry errors

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Genotype storage

• Single row per sample
• Genotype usability determined, pedigree change
  triggers a recheck
• Counts of validated parents and progeny
  maintained to indicate reliability of ID
  assignment
• Multiple genotypes per animal allowed
• Genotypes with invalid ID assignment stored
  but not usable
• DNA source (blood, semen, or hair) stored

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Genotype usability

• Genotype consistent with parents (few SNP
  conflicts)
• No genomic parent-progeny relationships not in
  pedigree found
• Not identical to another animal (unless identical
  twin, split embryo, or clone)
• X heterozygosity
• For bulls, low for X chromosome specific SNP
• For cows, high unless both X chromosomes from
  same ancestor

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Loading genotype database

• 50,972 SNP called
• Calling redone to provide genotypes for this set
• Many corrections required to make sample ID match
  
• Genotypes from Illumina, University of Missouri,
  University of Alberta, and Switzerland also
  included

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SNP selection

• MAF gt1 for at least 1 breed
• Based on MAF of 50 (Threshold more restrictive
  as MAF decreases)
• Call rate of gt90
• Parent-progeny conflicts of lt1
• Not a duplicate
• 43,385 SNP selected across breed

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Evaluation preparation

• Pedigree file created
• Checked for missing ancestors
• Pedigree requested for missing ancestors
• Canadian evaluations obtained for cows
• Type evaluations obtained for Holsteins

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Genomic evaluation calculation

• Automated evaluation system
• Jobs dispatched based on successful completion of
  prerequisites and processor availability
• Most traits run in parallel

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Genomic evaluation news

• Evaluations official
• Holstein and Jerseys (January 2009)
• Brown Swiss (August 2009)
• June 2009 trait changes
• Net Merit as sum of traits, not individual
• Holstein feet legs and rear teat placement
  added
• Current Interbull evaluation added at final
  selection-index step triannually

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Plans

• Monthly release of genomic evaluations if
  practical

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Summary

• Simplification of genotype processing
• Web-based nomination and validation
• Genotype calling by labs
• Database table to store genotypes
• Evaluation improvement
• Incorporation of current Interbull evaluation at
  end
• Canadian type evaluations for cows

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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)
• Brown Swiss Cattle Breeders Association (Beloit,
  WI)
• Agricultural Research Service, USDA