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

NAAB meeting April 2010 (2) Genotyped Holstein by run Run Date Old*Young** Total MaleFemaleMaleFemale Imputed (1471) * Animals with traditional evaluation ** Animals with no traditional evaluation

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

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

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

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

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

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

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

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

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

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

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)

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

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

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

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

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

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