1
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2
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- 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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3
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- 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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4
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5
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6
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- 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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7
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- 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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8
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- 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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9
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- 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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10
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- 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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11
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- 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
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12
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- 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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13
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- Automated evaluation system
- Jobs dispatched based on successful completion of prerequisites and
processor availability
- Most traits run in parallel
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14
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- 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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15
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- Monthly release of genomic evaluations if practical
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16
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- 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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17
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- 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
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