1. T. A. Cooper Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD Tabatha.cooper@ars.usda.gov NAAB meeting April 2010 (1) Genomic Database Update

2. NAAB meeting April 2010 (2) Genotyped Holstein by run Run Date Old*Young** Total MaleFemaleMaleFemale 0904760027119690194321944 09067883304911459297425365 09088512372812137367028047 09108568396513288479730618 10018974434814061603133414 10029378508615328762037412 1004 Imputed 97707300 (1471) 16002873241804 * Animals with traditional evaluation ** Animals with no traditional evaluation

3. NAAB meeting April 2010 (3) Genotyped Jersey by run Run Date Old*Young** Total MaleFemaleMaleFemale 1002197747911721973825 1004 Imputed 2072637 (97) 12502024161 * Animals with traditional evaluation ** Animals with no traditional evaluation

4. NAAB meeting April 2010 (4) Genotyped Brown Swiss by run Run Date Old*Young** Total MaleFemaleMaleFemale 1002116854179151416 1004 Imputed 118598 (47) 188311502 * Animals with traditional evaluation ** Animals with no traditional evaluation

5. NAAB meeting April 2010 (5) Data & Evaluation Flow Animal Improvement Programs Laboratory, USDA AI organizations, breed associations Dairy producers DNA laboratories samples genotypes nominations evaluations

6. NAAB meeting April 2010 (6) Genotype Processing l 2,000 New Genotypes a month l Four labs − GeneSeek − Genetic Visions − DNA LandMarks − GIVF

7. NAAB meeting April 2010 (7) l All animals should be nominated by the time sample reaches lab l Goal: Parents and Grandparents on every genotyped animal l Minimum: Valid ID Genotype Processing: Nomination

8. NAAB meeting April 2010 (8) l 62 edits that the genotypes must pass to be added to the database l Most common reasons a genotype fails − Low call rate − Parent / Progeny conflict − Possible split embryo / twin − Wrong gender − Breed Check − Switched samples Genotype Processing: Edits

9. NAAB meeting April 2010 (9) Continuous Updates l Pedigree changes update genotype usability daily l Harmonization with breed association important to maintain usability l Blanking a genotyped dam will make the genotype unusable l No automatic receipt of foreign pedigree updates

10. NAAB meeting April 2010 (10) Low call rate l 80% on X chromosome l 90% on autosomal chromosomes (43,382) l Labs generally do not send genotypes with low call rates

11. NAAB meeting April 2010 (11) Parent Progeny Conflict l Sire / Dam conflict l > 200 SNP conflicts l Sire / dam proposed if genotyped l Sire conflict - young animals from mixed flush l Sire conflicts represent $50,000 genotype cost

12. NAAB meeting April 2010 (12) split embryo / identical twin / clone l <1000 SNP differences considered identical l 98% similar, accounts for genotyping errors l Stored in clone table if valid l Animals registered as ETS or ETN (automatic) l Otherwise verification must come from requester

13. NAAB meeting April 2010 (13) Wrong Gender l > 50 heterozygous SNP on X (not male) l < 50 heterozygous SNP on X (not female) l Homozygous X female l Common ancestor (source of X)

14. NAAB meeting April 2010 (14) Source of X Jeff Erin Elegant BW Marshall Tanya Sam 12144058 Bellwood Mara Patron Mary Mark Sue Patron 14860763

15. NAAB meeting April 2010 (15) Breed Check l 622 SNP l Nearly monomorphic in 1 breed and have fewer than 30% of animals homozygous for that allele in another breed l An error when a higher number of conflicts for the reported breed than for another breed l > 10 SNP conflicts reported to requester, but remains usable l Higher conflicts for foreign animals

16. NAAB meeting April 2010 (16) Switched Samples l Sample pair with reversed parents l Switched at the lab (rare) l Switched at the farm

17. NAAB meeting April 2010 (17) Conflicts to Requester l Genotype conflicts reported to the requester immediately l Genotype remains stored in AIPL database as an unusable genotype until conflict is resolved l 2-3 days to fix conflicts before cutoff l Once a month all conflicts remaining in the system are sent to requesters

18. NAAB meeting April 2010 (18) Lab QC l SNP that have call rate <90% l SNP that have high parent-progeny conflicts l SNP that deviate from HW equilibrium l Labs have the opportunity to recluster genotypes

19. NAAB meeting April 2010 (19) Closing thoughts l Currently 477 animals with failed or conflicted genotypes l Big increase in volume when 3K becomes available