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AIPL Research Update

AIPL Research Update. Topic 1. Effect of bulk-tank SCC standard. DHI noncompliance by herd size – 1. 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.

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AIPL Research Update

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  1. AIPL Research Update

  2. Topic 1 Effect of bulk-tank SCC standard

  3. DHI noncompliance by herd size– 1 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– 2 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– 3 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 marketed milk– 1 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 marketed milk– 2 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 marketed milk– 3 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. Topic 3 Reporting of haplotypes with recessive effects on fertility

  15. Introduction • 5 haplotypes with recessive effects on fertility discovered • Additive effects small and in EBVs • All populations already carry these • At least 19 countries have “health” laws that exclude carriers of defects • Only countries that test are banned? • Import restrictions make little sense

  16. Recessive defect discovery • Check for homozygous haplotypes • 7 – 90 expected, but none observed • 5 of top 11 confirmed as lethal • 936 – 52,449 carrier sire  carrier MGS fertility records • 3.0 – 3.7% lower conception rates • Some slightly higher stillbirth rates • Confirmed brachyspina same way

  17. Haplotypes affecting fertility

  18. Additive and nonadditive effects* *Nonreturn rates or full gestation conception

  19. Carrier bulls with high fertility

  20. Using crossovers to fine map 75-marker haplotype (50K), about 5 Mbases Source Combined with source Suspect area Carrier Possible

  21. Crossovers used in fine mapping

  22. Detection without haplotyping • 3 methods to detect carriers • Use all genotypes and pedigrees • One at a time (ignore pedigree) • Find and test for causative mutation • Without vs. with haplotyping • 2.5% false positives, 0.05% false negatives • Similar to Georges et al. (2010) brachyspina haplotype test

  23. Detection with 3K genotypes* *500 carriers, 500 noncarriers, with imputation

  24. Conclusions • Recessive defects found in each breed (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 • Crossovers used for fine mapping

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

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