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Update on AIPL research since April 2009

This update provides information on the progress made in AIPL research since April 2009, including updates on the bovine genome, genotypes called, commercial labs, sample ID management, SNP selection, evaluation preparations, genomic evaluations, reliability calculation, Interbull plans, evaluation options, culling statistics, AM-PM factors, genetic resistance to Johne's disease, and cooperative studies.

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Update on AIPL research since April 2009

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  1. Update on AIPL research since April 2009 What’s new!

  2. Genomic news from the bovine g-nome Norman NDHIA Board – 2009 (2)

  3. News from the bovine g-nome Calling genotypes • Genotypes called by Tad Sonstegard, BFGL, through April 2009 • AIPL staff trained to run GenomeStudio • Cluster files shared with 4 commercial labs to allow call harmonization • Labs began providing genotypes in June

  4. News from the bovine g-nome Commercial labs • GeneSeek (Lincoln, NE) • Genetics & IVF Institute (Fairfax, VA) • Genetic Visions (Middleton, WI) • DNA LandMarks (Saint-Jean-sur-Richelieu, QC, Canada)

  5. News from the bovine g-nome Managing sample ID • Web query established for nominations • Indicates pedigree status • Designates nominator • Provides sample status, including rejection reasons • Query used by labs to convert sample ID to registration number and detect ID entry errors

  6. News from the bovine g-nome Genotype database • 50,972 SNP called • Calling redone to provide additional genotypes • Many corrections required to make sample ID match • Genotypes from Illumina, University of Missouri, University of Alberta, and Switzerland also included

  7. News from the bovine g-nome SNP selection • Call rate of >90% • Not a duplicate • Parent-progeny conflicts of <2% • Minor allele frequency of >1% • Heterozygosity within 20% of expected • For bulls, X heterozygosity of <5%

  8. News from the bovine g-nome Evaluation preparation • Pedigree file created • Checked for missing ancestors • Pedigree requested for missing ancestors • Canadian evaluations obtained for cows • Type evaluations obtained for Holsteins

  9. News from the bovine g-nome Genomic evaluations • Evaluations official • Holstein and Jerseys (January 2009) • Brown Swiss (August 2009) • June 2009 trait changes • Net merit calculated as sum of traits rather than as an individual trait • Holstein feet & legs and rear teat placement added • Current Interbull evaluation added at final selection-index step triannually

  10. News from the bovine g-nome Reliability calculation • Inversion and discounting • Gain in daughter equivalents times 0.6 • Simple approximation • Could be adjusted for breed or number of close relatives • Used in April 2009 to beat deadline

  11. News from the bovine g-nome Interbull plans • Convert genomic PTAs (August 2009) • Young bulls from France, Netherlands, and New Zealand • EU requires reliability of ≥50% for marketing • Combine using G-MACE (2010) • Proven bulls next year (2010) • Domestic and genomic evaluations computed 1–2 weeks earlier to meet Interbull deadlines • Currently genomics and MACE at same time

  12. News from the bovine g-nome Evaluation options • National • Include cows as predictors? • Include polygenic effect in model? • International • Conversion formulas for young bulls • G-MACE to exchange genomic breeding values • Direct multicountry genomic evaluation

  13. Culling statistics Norman NDHIA Board – 2009 (13)

  14. Culling status report • New annual AIPL Research Report by Norman, Wright, and Lombard available at AIPL web site (September 2009) • Based on destination (4) and termination (11) codes provided by DRPCs • Separate summaries by parity and breed • 6 breeds • 2 crossbred groups • Heterosis of >90% (crossbred, CB) • Heterosis of 50 to 90% (backcross, BC)

  15. Destination codes

  16. Termination codes

  17. Left herd but not sold for dairy

  18. AM-PM factors Norman NDHIA Board – 2009 (18)

  19. Cooperative research AM-PM factors • Purdue University (Mike Schutz) • Objectives • Derive factors to estimate daily yields from 1 record for 2X milking and 1 or 2 records for 3X milking • Compare factors derived by several methods for their accuracy in predicting true daily yield or somatic cell score (SCS)

  20. Progress to date AM-PM factors • Adjustment factors developed for Holstein and Jersey milk yield from 2X and 3X milkings • Preliminary Holstein and Jersey 2X AM-PM factors developed for fat, protein, and SCS

  21. Plans AM-PM factors • Verification of 2X AM-PM factors for fat and protein • Development and verification of 3X factors for fat and protein • Determination of whether effect of milking interval on somatic cell count is consistent enough to allow adjustment • All breeds combined for final estimation of adjustment factors

  22. Genetic resistance to Johne’s disease Norman NDHIA Board – 2009 (22)

  23. Johne’s disease Cooperative studies • Characteristics of milk ELISA scores and factors affecting scores • Antel BioSystems (Byrem, Norman) • Estimation of genetic parameters and transmitting ability for milk ELISA scores • University of Minnesota (Attala ... Cole)

  24. Johne’s disease Milk ELISA characteristics • Average score of 0.04 (±0.18) for 196,412 tests from 696 herds in 16 States from 2002 through 2008 • 3.2 and 6.1% positives based on cutoffs of 0.40 and 0.10 • Same average and SD for 42,778 scores from 25 more comprehensively tested herds in Michigan and Wisconsin • 3.0 and 5.6% positives

  25. Johne’s disease Milk ELISA(cont.) • Cows with multiple tests within parity (10%) • 95% negative for last test if 1st test negative • 52% positive for last test if 1st test positive • Cows with multiple tests across parities (27%) • 91% negative for last test if 1st test negative • 51% positive for last test if 1st test positive

  26. Johne’s disease Milk ELISA (cont.) • Unusually high percentage (44%) of untested cows removed from herd by end of current lactation likely indicates selection of which cows to test for Johne’s • Tested cows removed from herd • 15% of positive cows • 12% of negative cows • Further analysis needed to optimize usefulness of DHI records in evaluation of milk testing for Johne's

  27. Johne’s disease Factors affecting scores • Cow distribution by parity • Score distribution by days from calving to test • Birth and test seasons (four 3-mo seasons starting in January) normally distributed • Score distribution by year

  28. Johne’s disease Score factors(cont.) • Scores generally increased with year, parity, and test stage • Birth and test seasons nonsignificant • Low heritability (4%) • Moderate repeatability (26%)

  29. Johne’s disease Correlations • 185 Holstein AI sires with ≥50 daughters • PTA correlation with breeding value for ELISA score • Milk (0.08) • Fat (–0.06) • Protein (0.03) • Selection based on SCS, productive life, DPR, and net merit could improve resistance to Johne’s • SCS (-0.01) • Productive life (–0.19) • DPR (–0.15) • Net merit (–0.16)

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