T. A. Cooper and G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD Council on Dairy Cattle Breeding meeting April 2010 (1) Cow Adjustment and Genomic Database Update

Council on Dairy Cattle Breeding meeting April 2010 (2) Cow Adjustment

Council on Dairy Cattle Breeding meeting April 2010 (3) Gains in Reliability as of 2008

Council on Dairy Cattle Breeding meeting April 2010 (4) DGV vs Traditional PTA (Bulls) DGV – based on allele effects of all genotyped animals Traditional PTA – no genomics PA Milk (pounds) Milk (pounds) Bull DGVBull Traditional PTA

Council on Dairy Cattle Breeding meeting April 2010 (5) DGV vs Traditional PTA (Cows) DGV – based on allele effects of all genotyped animals Traditional PTA – no genomics PA Milk (pounds) Milk (pounds) Cow DGVCow Traditional PTA PA Milk (pounds) Milk (pounds) Cow DGVCow Traditional PTAAdjusted Traditional PTA

Council on Dairy Cattle Breeding meeting April 2010 (6) l high PTA values were causing the genomic predictions to suffer in accuracy l added information from genotyped cows was not increasing reliability Why reduce cow bias through adjustment?

Council on Dairy Cattle Breeding meeting April 2010 (7) Which animals were adjusted? l All genotyped and imputed cows l All genotyped animals including bulls, were affected by the adjustment made to the maternal portion of the parent average l Brown Swiss adjustments were not implemented due to low numbers of genotyped cows

Council on Dairy Cattle Breeding meeting April 2010 (8) How was the adjustment made? Daughter Equivalent (progeny) Std. Dev of Dereg M.S. (Milk) Cow Bull Birth year Milk (lbs.) Cow Bull Cow SD Adj Variance Adjustment Mean Adjustment

Council on Dairy Cattle Breeding meeting April 2010 (9) How was the adjustment made? l Deregressed Mendelian Sampling (MS) = (PTA-PA) / f(REL) l Adj. MS =.84*MS l Adj. PTA = f(REL)*(Adj. MS+ PA n ) + (1- f(REL)*PA n ) f(REL) = weight in PTA from own records and progeny

Council on Dairy Cattle Breeding meeting April 2010 (10) Effects of Cow Adjustment (Holstein) BiasRegressionGain REL NoYesDiffNoYesDiffNoYesDiff Milk (lb) Fat (lb) Protein (lb) Fat (%) Protein (%)

Council on Dairy Cattle Breeding meeting April 2010 (11) Effects of Cow Adjustment (Jersey) BiasRegressionGain REL NoYesDiffNoYesDiffNoYesDiff Milk (lb) Fat (lb) Protein (lb) Fat (%) Protein (%)

Council on Dairy Cattle Breeding meeting April 2010 (12) Example (Cow Milk PTA 1934  381) Progeny 1Jan PAApril PAProgeny2 Milk (pounds)

Council on Dairy Cattle Breeding meeting April 2010 (13) The future l Investigate solutions to the problem of not being able to compare genotyped and non- genotyped cows − Reduce heritability − Add dam-herd interaction − Varying heritability by herd − Other l With 3K chip, adjustments may need to vary by sub-population

Council on Dairy Cattle Breeding meeting April 2010 (14) Genomic Database

Council on Dairy Cattle Breeding meeting April 2010 (15) Genotyped Holstein by run Run Date Old*Young** Total MaleFemaleMaleFemale Imputed (1955) * Animals with traditional evaluation ** Animals with no traditional evaluation

Council on Dairy Cattle Breeding meeting April 2010 (16) Genotyped Jersey by run Run Date Old*Young** Total MaleFemaleMaleFemale Imputed (150) * Animals with traditional evaluation ** Animals with no traditional evaluation

Council on Dairy Cattle Breeding meeting April 2010 (17) Genotyped Brown Swiss by run Run Date Old*Young** Total MaleFemaleMaleFemale Imputed (63) * Animals with traditional evaluation ** Animals with no traditional evaluation

Council on Dairy Cattle Breeding meeting April 2010 (18) Genotype Processing l 2,000 New Genotypes a month l Four labs − GeneSeek − Genetic Visions − DNA LandMarks − GIVF

Council on Dairy Cattle Breeding meeting April 2010 (19) 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

Council on Dairy Cattle Breeding meeting April 2010 (20) l Genotypes must pass 62 edits 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

Council on Dairy Cattle Breeding meeting April 2010 (21) 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

Council on Dairy Cattle Breeding meeting April 2010 (22) 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

Council on Dairy Cattle Breeding meeting April 2010 (23) 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

Council on Dairy Cattle Breeding meeting April 2010 (24) 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

Council on Dairy Cattle Breeding meeting April 2010 (25) 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)

Council on Dairy Cattle Breeding meeting April 2010 (26) Source of X Jeff Erin Elegant BW Marshall Tanya Sam Bellwood Mara Patron Mary Mark Sue Patron

Council on Dairy Cattle Breeding meeting April 2010 (27) 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

Council on Dairy Cattle Breeding meeting April 2010 (28) Switched Samples l Sample pair with reversed parents l Switched at the lab l Switched at the farm

Council on Dairy Cattle Breeding meeting April 2010 (29) 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

Council on Dairy Cattle Breeding meeting April 2010 (30) Issues Reported to Lab for 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 re-cluster genotypes

Council on Dairy Cattle Breeding meeting April 2010 (31) Closing Thoughts l Currently 477 animals with failed or conflicted genotypes l Big increase in volume when 3K becomes available l Edits will remain with different thresholds for 3K data