Notes
Slide Show
Outline
1
Transition of genomic evaluation from a research project to a production system
2
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
3
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)
4
Before clustering adjustment
5
After clustering adjustment
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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
7
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
8
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
9
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
10
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
11
SNP selection
  • MAF >1% for at least 1 breed
  • Based on MAF of 50% (Threshold more restrictive as MAF decreases)
    • Call rate of >90%
    • Parent-progeny conflicts of <1%
  • Not a duplicate
  • 43,385 SNP selected across breed
12
Evaluation preparation
  • Pedigree file created
    • Checked for missing ancestors
    • Pedigree requested for missing ancestors
  • Canadian evaluations obtained for cows
  • Type evaluations obtained for Holsteins
13
Genomic evaluation calculation
  • Automated evaluation system
  • Jobs dispatched based on successful completion of prerequisites and processor availability
  • Most traits run in parallel
14
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
15
Plans
  • Monthly release of genomic evaluations if practical
16
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
17
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