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Identification and management of alleles impairing heifer fertility while optimizing genetic gain in cattle

Identification and management of alleles impairing heifer fertility while optimizing genetic gain in cattle. USDA-NIFA Award #2013-68004-20364. JF Taylor, DS Brown, MF Smith, RD Schnabel, SE Poock, JE Decker, FD Dailey, and DJ Patterson University of Missouri AL Van Eenennaam

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Identification and management of alleles impairing heifer fertility while optimizing genetic gain in cattle

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  1. Identification and management of alleles impairing heifer fertility while optimizing genetic gain in cattle USDA-NIFA Award #2013-68004-20364 JF Taylor, DS Brown, MF Smith, RD Schnabel, SE Poock, JE Decker, FD Dailey, and DJ Patterson University of Missouri AL Van Eenennaam University of California, Davis MM Rolf Oklahoma State University BP Kinghorn University of New England, NSW, Australia MD MacNeil Miles City, MT

  2. Broken Genes… • ~100 genes where one copy is functional and the other is broken • ~20 genes where the broken copy is a lethal mutation • Called Loss of Function mutations Science Vol. 335 no. 6070 pp. 823-828 DOI: 10.1126/science.1215040

  3. Broken Genes…

  4. Broken Genes… What happens when a broken gene is inherited from the father and the mother? • Genetic abnormality • Spontaneous abortion

  5. Broken Genes… Inconvenient Genetic Truth • Everybody has genetic defects!!! Even the most beautiful people in the world

  6. Broken Genes…

  7. Broken Genes… What happens when a broken gene is inherited from the sire and the dam? • Genetic abnormality • Spontaneous abortion

  8. Broken Genes… • Some we know about • Some we don’t KNOWN Even the most beautiful cattle in the world

  9. Genetic Defects • There are more than 35 genetic defects in cattle with a DNA test

  10. Silver Lining

  11. Silver Lining • DNA tests can now be developed in a few months • With DNA tests available, frequency of the known genetic defect rapidly decreases • Now we can manage genetic defects

  12. The Truth The Truth: Every Living Thing Is A Genetic Defect Carrier

  13. What to do before breeding • Test at-risk breeding stock for genetic defects • Do we know the pedigree of the animals? • Are there carriers in the pedigree?

  14. What to Do with an Abnormal Calf • Take a picture or video of affected calves • Freeze the entire animal if possible, otherwise preserve the abnormal body part • Obtain 40 hair bulbs from the calf, dam, and sire

  15. What to Do with an Abnormal Calf • Create a documented record of what happened • Breeders should contact their breed association and local veterinarian • Need intensive description of phenotype • The majority of abnormalities are caused by the environment, not genetics

  16. Broken Genes… What happens when a broken gene is inherited from the sire and the dam? • Genetic abnormality • Spontaneous abortion

  17. DNA Sequencing

  18. Variants Reducing Fertility • We will be sequencing 150 sires from 9 different breeds • We will discover hundreds of broken genes • Most embryonic lethals

  19. Variants Reducing Fertility • Sequencing completed to date:

  20. Variants reducing Fertility • We have already analyzed the genomes of 11 bulls

  21. Variants reducing Fertility • We have already analyzed the genomes of 11 bulls • Identified 176 possibly lethal alleles

  22. Validation

  23. Validation

  24. Genomic Prediction • Predictions are sums of marker effects • For lethal mutations • Homozygous normal: effect is 0 • Heterozygous lethal: effect is -qif • Allows publication of a fertility EPD

  25. Mate Selection Software • Avoid mating carriers of the same lethal mutation • Will also manage • Genetic merit • Genetic diversity • Built upon economic selection indexes

  26. The Old Paradigm • See abnormal calf • Bury calf

  27. The Current Paradigm • Report abnormal calves • Collect data • Create a test • Manage the defect

  28. The Genomics Paradigm? • Sequence influential AI sires • Create tests for LOF mutations • Manage the mutations while accounting for overall genetic merit

  29. Optimal practices

  30. Thank You! Questions? http://steakgenomics.blogspot.com

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