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Holstein, Jersey, and Brown Swiss Genomic Database Update

Learn how genotypes are processed and updated for Holstein, Jersey, and Brown Swiss animals with and without traditional evaluations. Stay informed about the data and evaluation flow, genetic processing standards, continuous updates, and common conflicts resolved in the lab QC.

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Holstein, Jersey, and Brown Swiss Genomic Database Update

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  1. Genomic Database Update

  2. Genotyped Holstein by run * Animals with traditional evaluation ** Animals with no traditional evaluation

  3. Genotyped Jersey by run * Animals with traditional evaluation ** Animals with no traditional evaluation

  4. Genotyped Brown Swiss by run * Animals with traditional evaluation ** Animals with no traditional evaluation

  5. Data & Evaluation Flow AI organizations, breed associations nominations samples evaluations ??? Animal Improvement Programs Laboratory, USDA Dairy producers samples samples genotypes DNA laboratories

  6. Genotype Processing • 2,000 New Genotypes a month • Four labs • GeneSeek • Genetic Visions • DNA LandMarks • GIVF

  7. Genotype Processing: Nomination • All animals should be nominated by the time sample reaches lab • Goal: Parents and Grandparents on every genotyped animal • Minimum: Valid ID

  8. Genotype Processing: Edits • 62 edits that the genotypes must pass to be added to the database • Most common reasons a genotype fails • Low call rate • Parent / Progeny conflict • Possible split embryo / twin • Wrong gender • Breed Check • Switched samples

  9. Continuous Updates • Pedigree changes update genotype usability daily • Harmonization with breed association important to maintain usability • Blanking a genotyped dam will make the genotype unusable • No automatic receipt of foreign pedigree updates

  10. Low call rate • 80% on X chromosome • 90% on autosomal chromosomes (43,382) • Labs generally do not send genotypes with low call rates

  11. Parent Progeny Conflict • Sire / Dam conflict • > 200 SNP conflicts • Sire / dam proposed if genotyped • Sire conflict - young animals from mixed flush • Sire conflicts represent $50,000 genotype cost

  12. split embryo / identical twin / clone • <1000 SNP differences considered identical • 98% similar, accounts for genotyping errors • Stored in clone table if valid • Animals registered as ETS or ETN (automatic) • Otherwise verification must come from requester

  13. Wrong Gender • > 50 heterozygous SNP on X (not male) • < 50 heterozygous SNP on X (not female) • Homozygous X female • Common ancestor (source of X)

  14. Source of X Bellwood BW Marshall Mara Elegant Patron Tanya Mary Jeff Mark Sam Sue Erin Patron 12144058 14860763

  15. Breed Check • 622 SNP • Nearly monomorphic in 1 breed and have fewer than 30% of animals homozygous for that allele in another breed • An error when a higher number of conflicts for the reported breed than for another breed • > 10 SNP conflicts reported to requester, but remains usable • Higher conflicts for foreign animals

  16. Switched Samples • Sample pair with reversed parents • Switched at the lab (rare) • Switched at the farm

  17. Conflicts to Requester • Genotype conflicts reported to the requester immediately • Genotype remains stored in AIPL database as an unusable genotype until conflict is resolved • 2-3 days to fix conflicts before cutoff • Once a month all conflicts remaining in the system are sent to requesters

  18. Lab QC • SNP that have call rate <90% • SNP that have high parent-progeny conflicts • SNP that deviate from HW equilibrium • Labs have the opportunity to recluster genotypes

  19. Closing thoughts • Currently 477 animals with failed or conflicted genotypes • Big increase in volume when 3K becomes available

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