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- Illumina BovineSNP50™ BeadChip developed
- Accuracy of genomic information assessed by using 2004 evaluations of
bulls born before 2000 to predict 2009 evaluations of young bulls
- Unofficial genomic evaluations of bull calves provided to industry
beginning in April 2008
- Jersey results released in October 2008
- New results released every 2 months
- Nearly 23,000 animals genotyped through Mar. 2009
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- Single-nucleotide polymorphism
- Place on the chromosome where animals differ in the nucleotides (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 both alleles well
represented in population
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4
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- DNA extracted from blood, hair, or semen
- ~40,000 genetic markers (SNPs) evaluated
- For each SNP, difference in PTA estimated between animals with 1 allele
compared to the other allele
- Genomic evaluation combines SNP effect estimates with existing PA or PTA
- Genomic data contribute ~11 daughter equivalents to reliability
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- Participating AI organizations have 5-year exclusive right to evaluate
bulls genomically
- Each AI organization genotypes first-choice flushes, thereby usually
avoiding duplicate genotypes
- Web-based system collects nominations
- Avoid duplication
- Confirm validity of ID and pedigree
- Associate sample ID with animal ID
- Breed associations offer cow genotyping service
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- Nominate animal for genotyping; confirm not already genotyped
- Collect hair, blood, or semen from animal
- Blood not suitable for twins
- Send to laboratory for extraction
- Transfer DNA to BeadChip (12 samples/chip) for 3-day genotyping process
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- Read red/green intensities from chip
- Transfer intensity files to AIPL for calling genotypes
- Check genotypes for duplicates, parent-progeny conflicts, and wrong sex
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- 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 (some do extraction only)
- 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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- Sample doesn’t provide adequate DNA quality or quantity
- Genotype has many SNPs that can’t 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 true parent
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11
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- Accurate genomic evaluations require estimates of SNP effects
- Evaluations with high reliability provide the most information
- Recent animals are more useful than ones from earlier generations
- Reliability of genomic evaluations increases with number of predictor
animals
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12
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- Calculate parent average (PA) based only on genotyped animals with best
linear unbiased prediction
- Combine traditional PA (or evaluation) with genomic PA and evaluation
using selection index weights
- Update traditional evaluation with additional information from genomics
- Reliability from inverse of genomic relationship matrix
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- Genotype can be thought of as source of information like parents,
progeny, and records
- Official PTA that include a genomic contribution are identified
- One genotype used to calculate genomic evaluations for all 29 traits
- Genomic evaluations used the same as traditional PTA
- Expected to increase rate of genetic improvement because of a large
decrease in generation interval
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16
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17
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18
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19
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20
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- Semex
- Participated since beginning of genomics research
- Contributed genotypes to providing a important increase in accuracy for
first test
- Genotypes will be shared between AIPL and Canadian Dairy Network
- AIPL and University of Guelph collaboration
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22
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- Same set of predictor animals used in Canada and U.S. so that
evaluations of genotyped animals have same accuracy
- Canada expects official release of genomic evaluations in August 2009
- Common procedures between 2 countries assist in industry acceptance
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- AI organizations determine which young bulls to buy
- Considered in selection of mating sires
- Impact on bull dam selection will increase
- Used to market semen from 2-year-old bulls
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- Genomic evaluations became official
- Genotyped ancestors contribute their evaluations to descendants
- Evaluations of all genotyped females are public
- Evaluations of males enrolled with NAAB or ≥24 months old are public
- Young-bull genomic evaluations may be shared among AI organizations or
disclosed by owner
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- Genomic evaluations calculated approximately every 2 months
- Evaluations of animals that already have an official evaluation not
released
- Evaluations of new animals distributed to owners
- Females by breed associations
- Males by NAAB
- Usually 1,000–2,000 new genotypes included
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- Nomination establishes a requester who receives the genomic evaluation
- Requesters
- 7 participating AI organizations
- U.S. and Canadian Holstein associations
- American Jersey Cattle Association
- Some laboratories
- Requesting AI organization can agree to share an evaluation with other
AI organizations
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- Evaluations of all females sent to respective breed associations for
distribution to owners
- NAAB distributes bull evaluations to owners and manages sharing of
evaluations among AI organizations
- Genomic evaluations of animals with official evaluations released as
unofficial at updates between official evaluations
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- Young-bull evaluations with accuracy of early 1st-crop evaluations
- AI organizations marketing genomically evaluated 2-year-olds
- Bull dams likely to be required to be genotyped
- Rate of genetic improvement likely to increase by up to 50%
- Progeny-test programs changing
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- Calculate SNP effects with each of 3 annual traditional evaluations
- Calculate genomic evaluations once or more between traditional
evaluations
- Recalculate SNP effects if significant number of predictor animals
added
- May use existing SNP effects if only young animals added
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- Require bar codes on sample containers to reduce errors and improve lab
efficiency
- Require animals be enrolled with breed association before DNA sample
collected
- Process genotypes frequently; check for and report conflicts as received
- Reduce processing time by improving efficiency of genotype calling
either by laboratories or at AIPL
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- Scanner reads chip recording intensities of red and green
- Software converts those to AA, AB, or BB
- Genotype is missing if assignment is uncertain
- Accuracy can be improved by adjusting for variation in intensity due to
SNP and animal
- Techniques to automate adjustment are underway
- Manual intervention can increase accuracy of calling with current
software
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- Genotype more predictor bulls
- Automatic increase as bulls in waiting receive traditional evaluations
- Increase number of SNPs used
- Reach 1,500 Brown Swiss through foreign collaboration?
- Increase genotyped Jerseys from both domestic animals and possible
foreign collaboration
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- All major dairy countries investigating genomic selection
- Interbull meeting January 2009 discussed how genomic evaluations should
be integrated
- AI organizations need to find balance between competitive benefits from
treating genotypes as proprietary versus sharing
- Importing countries must change rules to allow for genomically evaluated
young bulls
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- Determine inheritance of individual chromosome segments (haplotyping)
- May allow better tracking of QTL
- Approximate genotypes of missing ancestors to increase predictor
population
- Increase number of SNPs or even use entire DNA sequence
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- Extraordinarily rapid implementation of genomic evaluations
- Young bull acquisition and marketing now based on genomic
evaluations
- Genomic evaluations may allow more cows from commercial herds to be used
as bull dams
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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)
- Agricultural Research Service, USDA
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