1	Transition of genomic evaluation from a research project to a production system
2	Genomic evaluation system Provides timely evaluations of young bulls for purchasing decisions Increases accuracy of evaluations of bull dams Assists in selection of service sires, particularly for low-reliability traits
3	Obtaining genotypes Collect tissue sample (hair and blood most common for calves) Extract DNA Bind DNA to chip (12 samples/chip) Scan chip to create intensity files Call genotypes (GenomeStudio software)
4	Before clustering adjustment
5	After clustering adjustment
6	Calling genotypes Genotypes called by Tad Sonstegard, BFGL, through April 2009 AIPL staff trained to run GenomeStudio Cluster files shared with 4 commercial labs to promote call harmonization Labs began providing genotypes in June
7	Managing sample ID Web query established for nominations Indicates missing pedigrees Designates who receives evaluation Provides sample status, including rejection reasons Query used by labs to convert sample ID to registration number and detect ID entry errors
8	Genotype storage Single row per sample Genotype usability determined, pedigree change triggers a recheck Counts of validated parents and progeny maintained to indicate reliability of ID assignment Multiple genotypes per animal allowed Genotypes with invalid ID assignment stored but not usable DNA source (blood, semen, or hair) stored
9	Genotype usability Genotype consistent with parents (few SNP conflicts) No genomic parent-progeny relationships not in pedigree found Not identical to another animal (unless identical twin, split embryo, or clone) X heterozygosity For bulls, low for X chromosome specific SNP For cows, high unless both X chromosomes from same ancestor
10	Loading genotype database 50,972 SNP called Calling redone to provide genotypes for this set Many corrections required to make sample ID match Genotypes from Illumina, University of Missouri, University of Alberta, and Switzerland also included
11	SNP selection MAF >1% for at least 1 breed Based on MAF of 50% (Threshold more restrictive as MAF decreases) Call rate of >90% Parent-progeny conflicts of <1% Not a duplicate 43,385 SNP selected across breed
12	Evaluation preparation Pedigree file created Checked for missing ancestors Pedigree requested for missing ancestors Canadian evaluations obtained for cows Type evaluations obtained for Holsteins
13	Genomic evaluation calculation Automated evaluation system Jobs dispatched based on successful completion of prerequisites and processor availability Most traits run in parallel
14	Genomic evaluation news Evaluations official Holstein and Jerseys (January 2009) Brown Swiss (August 2009) June 2009 trait changes Net Merit $ as sum of traits, not individual Holstein feet & legs and rear teat placement added Current Interbull evaluation added at final selection-index step triannually
15	Plans Monthly release of genomic evaluations if practical
16	Summary Simplification of genotype processing Web-based nomination and validation Genotype calling by labs Database table to store genotypes Evaluation improvement Incorporation of current Interbull evaluation at end Canadian type evaluations for cows
17	Financial support National Research Initiative grants, USDA NAAB (Columbia, MO) ABS Global (DeForest, WI) Accelerated Genetics (Baraboo, WI) Alta (Balzac, AB) Genex (Shawano, WI) New Generation Genetics (Fort Atkinson, WI) Select Sires (Plain City, OH) Semex Alliance (Guelph, ON) Taurus-Service (Mehoopany, PA) Holstein Association USA (Brattleboro, VT) American Jersey Cattle Association (Reynoldsburg, OH) Brown Swiss Cattle Breeders’ Association (Beloit, WI) Agricultural Research Service, USDA