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Title: Dairy cattle genomics evaluation program update

item Wiggans, George
item Vanraden, Paul
item Cooper, Tabatha

Submitted to: National Breeders Roundtable Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 4/29/2011
Publication Date: 5/5/2011
Citation: Wiggans, G.R., Van Raden, P.M., Cooper, T.A. 2011. Dairy cattle genomics evaluation program update. National Breeders Roundtable Proceedings. St. Louis, MO, May 5–6, pp. 31-41.

Interpretive Summary:

Technical Abstract: Implementation of genomic evaluation has caused profound changes in dairy cattle breeding. All young bulls bought by major artificial-insemination organizations now are selected based on these evaluation. Evaluation reliability can reach ~75% for yield traits, which is adequate for marketing semen of 2-yr-old bulls. Shortened generation interval from using genomic evaluations is the most important factor in increasing genetic improvement. Genomic evaluations are based on 42,503 single nucleotide polymorphisms (SNP) genotyped with technology that became available in 2007. The first unofficial USDA genomic evaluations were released in 2008 and became official for Holsteins, Jerseys, and Brown Swiss in 2009. Evaluation accuracy has increased steadily from including additional bulls with genotypes and traditional evaluations (predictor animals). Some of that increase occurs automatically as young genotyped bulls receive a progeny-test evaluation at 5 yr of age. Cow contribution to evaluation accuracy is increased by reducing mean and variance of their evaluations so that they are similar to bull evaluations. Integration of US and Canadian genotype databases was critical to achieving acceptable initial accuracy and continues to benefit both countries. Genotype exchange with other countries added predictor bulls for Brown Swiss and will add bulls for Holstein. In 2010, a low-density chip with 2,900 SNP and a high-density chip with 777,962 SNP were released. The low-density chip has increased greatly the number of animals genotyped and is expected to replace microsatellites in parentage verification. The high-density chip can increase evaluation accuracy by better tracking of loci responsible for genetic differences. To integrate information from chips of various densities, a method to impute missing genotypes was developed based on splitting each genotype into its maternal and paternal haplotypes and tracing their inheritance through the pedigree. The same method is used to impute genotypes of nongenotyped dams based on genotyped progeny and mates. Reliability of resulting evaluations is discounted to reflect errors inherent in the process. Gains in reliability from genomics above parent average ranged from 2.7 to 47.6 percentage units for Holsteins, 9.6 to 29.2 percentage units for Jerseys, and 3.0 to 25.8 percentage units for Brown Swiss demonstrating the contribution to accuracy from genomics.