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Genomics: what we have and what is coming

Genomics: what we have and what is coming. How the system works. Studs and Breeds nominate animals through AIPL web site Hair, blood, Semen, or extracted DNA sent to 1 of 4 Labs Genotypes sent to AIPL monthly

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Genomics: what we have and what is coming

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  1. Genomics: what we have and what is coming

  2. How the system works • Studs and Breeds nominate animals through AIPL web site • Hair, blood, Semen, or extracted DNA sent to 1 of 4 Labs • Genotypes sent to AIPL monthly • Starting in April monthly updates will be released on the first Tuesday of most months • All official evaluations updated at tri-annual traditional runs

  3. Recent improvements • Studs may submit pedigree and nominate in batch files • Pedigree from CAN, AUS, GBR automatically collected from web sites • Polygenic effect set at 10% to include genetic variation not captured by SNP • Net Merit calculated from component traits, not analyzed as a separate trait

  4. Changes planned for April • Deviations of predictor cows adjusted to be like bulls with similar reliability to improve their contribution to accuracy • Genotypes of dams of genotyped animals imputed to add predictor animals • Sum of genomic relationships of each animal with the predictor animals used to improve estimation of Reliability

  5. 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 • Inheritance of haplotypes tracked • Accuracy of imputation improves with number of progeny • Crossovers during meiosis contribute to uncertainty

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

  7. Cow Problem • Evaluations of elite cows appear biased upward • Cutoff studies show only a small benefit from including cows as predictors • Reducing heritability would reduce the problem but appears unacceptable • Adjustment of cow evaluations investigated

  8. 2500 2000 1500 Cow Std. Dev of Deregressed Value (Milk) Bull 1000 500 0 0.4 0.6 1.0 2.5 Daughter Equivalent (progeny) SD of Cow Deviation from PA

  9. 1000 800 600 400 Cow Milk (lbs.) Cow SD Adj 200 Bull 0 -200 2000 2001 2002 2003 2004 2005 2006 2007 -400 Birth year Mean of Cow Deviation from PA

  10. Cow Adjustment Parameters • PTA calculated from adjusted deregressed values and used in PA • High reliability bulls (99%) not adjusted • Adjusted values used to calculate % traits

  11. Effect of Adjustment on Holstein

  12. Effect of Adjustment on Jersey

  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 • Adjusted PTA will be reported in XML traditional fields

  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. Reliabilities for HO born ≥ 2005

  16. Bulls First Traditional Eval. Jan., 2010

  17. Cows First Traditional Eval. Jan., 2010

  18. Accommodating chip diversity • Impute to highest density • Calculate SNP effects for all HD SNP • Mechanism for accounting for loss in accuracy due to imputation error needed • Percent missing may be enough • Only observed genotypes stored in database • Evaluations labeled as to source of genotype

  19. Illumina 3K chip • SNP chosen to • Be evenly spaced • Include some Y specific SNP • Include 90 SNP for breed determination • Expect to impute genotypes for 43,385 SNP with high accuracy • Expect breeds to use 3K chip to replace microsatellites for parentage verification • Breeds allowed to genotypes bulls for parentage only.

  20. Proposed Stud use of 3K • Genomic evaluation accuracy adequate for first stage screening • HD genotyping reserved for bulls acquired. • Confirm ID • Second stage selection • Lower cost enables genotyping more candidates • Savings could be applied to genotype more predictor bulls to meet EuroGenomics challenge

  21. HD chip • Includes current 43,385 SNP so can replace 50K chip in current evaluations • 5,000+ genotypes at HD required to support imputation of HD from current 50K SNP • Expected gain in Rel < 2 • May allow HO genotypes to contribute to accuracy of JE & BS genomic evaluations

  22. HD chip (Cont.) • Could share cost of HD genotyping with Europe to ensure enough animals to enable accurate imputation • Trend is toward higher densities. • Continued genotyping at 50K may be shortsighted • May allow reduction in polygenic effect giving increased accuracy

  23. Will data recording survive • Progeny test no longer required to market bulls • In 2013, new entrants may have no data collection expense • Loss in accuracy of SNP effect estimates occurs over time • How much data is needed?

  24. Assumptions About Future Data RELtrad of foreign bulls multiplied by square of genetic correlation (.9)2

  25. Reliability from Additional Data 7,500 N. American bulls = 1500 / year over next 5 years

  26. What replaces the PT program • G bulls will have 1,000s of daughters in their early Trad evaluations • Milk recording is justified for management information • Type data may come from breeder herds because they use G bulls • Data on new traits will require investment

  27. Data into National Evaluations • Progeny Test herds could become Data Supply herds • Data acquisition could be supported by a fee based on bulls genotyped • Plan must be perceived as fair by all industry players • Quality Certification model could apply

  28. Questions • How to match accuracy of evaluations from EuroGenomics • Should young bull purchases be based on 3K genotypes • How will continued flow of data into genetic evaluations be assured

  29. 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) • American Brown Swiss Association (Beloit, WI) • Agricultural Research Service, USDA

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