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Routine genomic predictions

Routine genomic predictions. Getting started. Select animals to genotype Assign identification to animals Collect tissue samples Extract DNA Check DNA quality and standardize concentration on mother plate Propagate to daughter plates. Infinium ® II assay protocol. © 2006 Illumina, Inc.−

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Routine genomic predictions

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  1. Routinegenomicpredictions

  2. Getting started • Select animals to genotype • Assign identification to animals • Collect tissue samples • Extract DNA • Check DNA quality and standardize concentration on mother plate • Propagate to daughter plates

  3. Infinium® II assay protocol © 2006 Illumina, Inc.− For research use only Source: Infinium® II Assay Workflow, Illumina® SNP Genotyping

  4. Evaluation workflow • Check genotypes for inheritance errors • Calculate genomic relationships • Infer missing genotypes • Estimate SNP effects

  5. Evaluation workflow – cont. • Combine genomic information with parent average • Based on gain from genomics over parent average for animals with genotypes • Apply to all traits • Distribute results

  6. First genomic evaluation • 750 animals nominated for genotyping • Over 5,285 predictor bulls from US and Canada • Embryo flushes • AI organization with first choice arranged for genotyping • Genotypes shared by agreement between studs

  7. First genomic evaluation – cont. • Calves must have unique ID • Holstein offers Easy-ID program • Samples sent to GeneSeek for extraction • BFGL genotyped animals with chips purchased through cooperative research and development agreement • AIPL calculated genomic evaluations

  8. First genomic evaluation – cont. • April distribution to cooperators • Evaluations sent to AI organizations that paid for chip • Evaluation mailed to US owner of animals • Future schedule at least every 2 months

  9. Proposed mailer (text) • Recently you provided a blood sample (or other DNA) for bull HOUSA00000000001, GENOMICS EXTRAORDINAIRE-ET (born 2001). That sample was analyzed with a new technology that labels small segments of the chromosomes. Then the contribution of each of those segments to the overall genetic merit of the animal was estimated. The resulting genomic predicted transmitting ability (PTA) is a much more accurate estimate of the animal’s genetic merit than is parent average alone. On the reverse side of this letter, new genomic PTAs are shown along with the animal’s current official USDA evaluation for a number of traits. These evaluations should not be used in advertising. More research and education is needed before genomic predictions can replace official PTAs, and methods to incorporate genomic information into evaluations of relatives that have not been genotyped are being developed. Scientific articles describing the statistical methods and results from both simulated and real genomic data are listed in Changes to Evaluation System (April 2008) (http://aipl.arsusda.gov/reference/changes/eval0804.html). Genomic predictions for about 730 animals (mostly calves) are being distributed to owners as identified by the breed associations and to organizations that paid for genotyping (for example, an artificial-insemination company) to aid in selection decisions. The artificial-insemination organizations that contributed to this research have a 5-year period of exclusive rights to obtain genomic evaluations of males. Evaluations of females will be made available to anyone who provides a genotype through a cooperating organization.

  10. Proposed mailer (tables) Health traits

  11. Proposed mailer (tables) – cont. Yield traits

  12. Proposed mailer (tables) – cont. Calving traits

  13. Proposed mailer (tables) – cont. Type traits etc.

  14. Future plans • Use genomic information to update evaluations of animals not genotyped (3 times each year) • Genomic evaluations calculated and released more frequently (monthly? weekly?) • Bull evaluations made public when bull enrolled with NAAB • Cow evaluations made public immediately at USDA web site • January 2009 target for public release

  15. Genomic selection (New Zealand) • Identify top 30,000 bull calves annually based on parent average • Genotype by 6 days old with 768 SNP • Genotype top 500 bull calves with 50k SNP chip • Keep top 100 bull calves

  16. Genomic selection (NZ)– cont. • At 1 year, limited progeny test to check for undesirable recessives • At 2 years, market as part of DNA team • When progeny tested, graduate best to progeny-proven team

  17. Research topics • Differential inclusion of X-chromosome effects to predict bulls vs cows • Contribution of cows to accuracy of genomic prediction • Benefit of genotyping more predictor bulls • Optimum methods for combining genomic and current evaluation

  18. Research topics– cont. • Practicality of screening and parentage verification with low-cost, low-SNP number assay • Potential of freely sharing enough SNP for accurate parentage discovery • Computational methods to improve accuracy, such as haplotyping

  19. Summary • Genomic prediction has great promise • Extensive changes in bull acquisition and marketing and in cow selection expected  • Routine genotyping and validation will become industry rather than research responsibilities

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