Unraveling Recessive Fertility Effects: Detection and Implications

1. Reporting of Haplotypes with Recessive Effects on Fertility

2. Introduction • Fivehaplotypes with recessive effects on fertility discovered • Additive effects small and in EBVs • All populations already carry these • At least 19 countries have ‘health’ laws excluding carriers of defects • Only countries that test are banned? • Import restrictions make little sense

3. Recessive Defect Discovery • Check for homozygous haplotypes • 7 to 90 expected but none observed • 5 of top 11 confirmed as lethal • 936 to 52,449 carrier sire by carrier MGS fertility records • 3.0% to 3.7% lower conception rates • Some slightly higher stillbirth rates • Confirmed Brachyspina same way

4. Haplotypes Affecting Fertility

5. Additive and Nonadditive Effectson nonreturn rates or full gestation conception

6. Carrier Bulls with High Fertility

7. Using Crossovers to Fine Map 75 marker haplotype (50K), about 5 Mbases Source Combined With Source Suspect Area Carrier Possible

8. Crossovers used in Fine Mapping

9. 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 positive, 0.05% false neg • Similar to Georges et al (2010) Brachyspinahaplotype test

10. Detection with 3K Genotypes500 carriers, 500 noncarriers, with imputation

11. Conclusions • Recessive defects found in each breed (HH1, HH2, HH3, JH1, BH1) • Officially reported in August • Most embryo losses < 60 days • Breeders should select for fertility, not against individual defects, and mate carriers to noncarriers • Crossovers used for fine mapping