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Genomic Evaluations

Genomic Evaluations. Structure of genomic evaluations. All genotypes shared with Canada Holstein, Jersey, Brown Swiss included Participants 3 Breed Associations 7 major studs and 5 small ones 4 genotyping laboratories Monthly evaluations. Bull genomic evaluations.

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Genomic Evaluations

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  1. Genomic Evaluations

  2. Structure of genomic evaluations • All genotypes shared with Canada • Holstein, Jersey, Brown Swiss included • Participants • 3 Breed Associations • 7 major studs and 5 small ones • 4 genotyping laboratories • Monthly evaluations

  3. Bull genomic evaluations • Designated studs have exclusive right to receive genomic evaluations of bulls until May 2013

  4. Genotyped Holstein by run * Animals with traditional evaluation ** Animals with no traditional evaluation

  5. How the system works • Studs and breeds nominate animals through web site • Hair, blood, semen, or extracted DNA sent to Labs • Genotypes sent to AIPL monthly • Evaluation updates provided to studs and breeds monthly • All evaluations updated at tri-annual traditional runs

  6. Conflict checking • Parent-progeny conflicts detected • Sex and breed checked • Conflicts reported to lab and requester for resolution

  7. Recent changes • Genotypes for some dams imputed from progeny • Traditional evaluations of genotyped cows adjusted to improve accuracy of genomic evaluations

  8. Imputation • Determine an animal’s genotype from genotypes of its parents and progeny • Genotype separated into sire and dam contributions. Identifies the allele on each member of a chromosome pair

  9. O-Style Haplotypeschromosome 15

  10. Imputation (cont.) • Inheritance of haplotypes tracked • Accuracy of imputation improves with number of progeny • Crossovers during meiosis contribute to uncertainty

  11. Cow Adjustment • Evaluations of elite cows biased upward • Cutoff studies showed little benefit from including cows as predictors • Reducing heritability would reduce the problem but industry is reluctant to do so • Adjustment of cow evaluations implemented

  12. Effect of Adjustment on Holstein

  13. Cow Adjustment Summary • Increased reliability of genomic predictions • Genomic evaluations of the top cows, top young bulls, and top heifers decreased • Among bulls, foreign bulls with a high proportion of genotyped daughters had largest changes

  14. 4000 3500 3000 2500 Number of Bulls 2000 1500 1000 500 0 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 Milk REL Reliability for young HO Bulls N = 15,226

  15. Chip diversity • Low cost chip with 3072 (3K) SNP expected this summer • High density chip (860K) in development • Version 2 of BovineSNP50 announced with changes in SNP list

  16. Accommodating chip diversity • Impute to higher density • Calculate effects for all high density SNP • Mechanism for accounting for loss in accuracy due to imputation error needed • Percent missing genotypes • Only observed genotypes stored in database • Evaluations labeled as to source of genotype

  17. Illumina 3K chip • SNP chosen • 3072, evenly spaced • Some Y specific SNP • 90 SNP for breed determination • Expect to impute genotypes for 43,382 SNP with high accuracy • Expect breeds to use 3K chip to replace microsatellites for parentage verification • Breeds allowed to genotype bulls for parentage only

  18. Proposed stud use of 3K chip • Accuracy adequate for first stage screening • Higher density genotyping reserved for bulls acquired. • Confirm ID • Second stage selection • Maximize accuracy of evaluation used for marketing • Genotype more candidates

  19. Current research • Prepare for Interbull validation of genomic evaluations • Improve accuracy of imputation • Refine cow adjustment for use with 3K chip • Evaluate how to restore comparability between evaluations of genotyped and non-genotyped cows • Investigate ways to increase accuracy by increasing predictor population

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