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AIPL Research Update

AIPL Research Update. Topic 1. Effect of bulk-tank SCC standard in DHI and Federal Milk Orders. DHI noncompliance by herd size – NMPF. 3 of 5 consecutive BTSCC tests exceeding a limit of 750,000 cells/mL 600,000 cells/mL 500,000 cells/mL

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AIPL Research Update

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  1. AIPL Research Update

  2. Topic 1 Effect of bulk-tank SCC standard in DHI and Federal Milk Orders

  3. DHI noncompliance by herd size–NMPF 3 of 5 consecutive BTSCC tests exceeding a limit of 750,000 cells/mL 600,000 cells/mL 500,000 cells/mL 400,000 cells/mL

  4. DHI noncompliance by herd size–NDHIA 4 consecutive 3-mo geometric mean BTSCC exceeding a limit of 750,000 cells/mL 600,000 cells/mL 500,000 cells/mL 400,000 cells/mL

  5. DHI noncompliance by herd size–NMC 3-mo geometric mean BTSCC exceeding limit plus next BTSCC test exceeding a limit of 750,000 cells/mL 550,000 cells/mL

  6. FMO noncompliance by milk sold–NMPF 3 of 5 consecutive BTSCC tests exceeding a limit of 750,000 cells/mL 600,000 cells/mL 500,000 cells/mL 400,000 cells/mL

  7. FMO noncompliance by milk sold–NDHIA 4 consecutive 3-mo geometric mean BTSCC exceeding a limit of 750,000 cells/mL 600,000 cells/mL 500,000 cells/mL 400,000 cells/mL

  8. FMO noncompliance by milk sold–NMC 3-mo geometric mean BTSCC exceeding limit plus next BTSCC test exceeding a limit of 750,000 cells/mL 550,000 cells/mL

  9. Topic 2 Genotyping

  10. New genotypes 6,000 3K – 42,512 total 5,000 4,000 3,000 2,000 1,000 50K and HD – 77,553 total 0 9-10 10-10 11-10 12-10 1-11 2-11 3-11 4-11 5-11 6-11 7-11 Totals as of July 2011

  11. Sex distribution – August 2010 Males 61% Females 39% All genotypes

  12. Sex distribution – July 2011 Females 58% Males 42% All genotypes

  13. 3K sample characteristics • 93% of 3K genotypes are from females • 3K sample types include • Hair (79%) • Blood (10%) • Nasal (10%) • Semen (1%)

  14. Low-density chip (BovineLD–6,909 SNPs) Data first available in October 2011 Evaluations coming in November 2011 Expected to replace 3K chip because of greater genotyping accuracy 98.9% for Holsteins (versus 95.9% for 3K) 98.2% for Jerseys (versus 94.6% for 3K) 97.9% for Brown Swiss (versus 93.9% for 3K) Repeatabilities also higher with LD genotypes

  15. Improving pedigree accuracy As genotypes are received, maternal grandsires (MGS) are checked, and those unlikely are reported When MGS is unlikely, other males are examined, and the most likely alternatives are provided

  16. Topic 3 Discovery of haplotypes with recessive effects impacting fertility

  17. Dominant-recessive example Black versus red coat color in Holsteins Assume frequency is 90% (.90) for black allele B Then, homozygous black (BB) frequency is expected to be 81% (.90 × .90) Homozygous red (bb) frequency is expected to be 1% (.10 × .10) Heterozygous black (Bb) frequency is expected to be 18% (2 × .90 × .10); i.e., red carriers

  18. Similar inheritance • 5 haplotypes with recessive effects impacting fertility discovered • Additive effects small and already in evaluations • Most (or all) populations already carry these • At least 19 countries have “health” laws that exclude carriers of defects • Irony: Only countries that test are banned • Thus, import restrictions make little sense

  19. Recessive defect discovery • Check for homozygous haplotypes • 7 – 90 expected, but 0 observed • 5 of top 11 haplotypes confirmed as lethal • 936 – 52,449 carrier sire  carrier MGS fertility records • 3.0 – 3.7% lower conception rates • Confirmed brachyspina same way

  20. Haplotypes impacting fertility

  21. Effect on fertility Determine fertility differences between matings that could have produced a recessive versus those that could not have 3 types of bulls: tested carriers, tested noncarriers, and not tested 9 types of sire × MGS matings (3 × 3) Subtract fertility effects for animals with carrier sire and carrier MGS from those for animals with noncarrier sires

  22. Additive and nonadditive decreases* *Nonreturn rates or full gestation conception

  23. Carrier bulls with high fertility

  24. Conclusions • Recessive defects found in 3 breeds (HH1, HH2, HH3, JH1, BH1) • Officially reported in August • Most embryo losses at<60 days • Breeders should select for fertility (not against individual defects) and mate carriers to noncarriers • Research underway to fine map the recessives

  25. Acknowledgment Paul VanRaden (AIPL) discovered the haplotypes that affect fertility with the assistance of: Dan Null (AIPL) Katie Olson (NAAB), and Jana Hutchison (AIPL)

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