Dairy genomics in application

Authors: Wiggans, George; Vanraden, Paul; Cooper, Tabatha

Submitted to: Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 5/26/2011
Publication Date: 5/17/2011
Citation: Wiggans, G.R., Van Raden, P.M., Cooper, T.A. 2011. Dairy genomics in application. Minnesota Dairy Health Conference, St. Paul, MN, May 17-19, pp 29-38.

Interpretive Summary: The implementation of genomic evaluation for dairy cattle has caused profound changes in dairy cattle breeding. The reliability of those evaluations can reach around 75% for yield traits. This technology, which resulted from an international consortium of government, university, and industry cooperators, became available in December 2007, and the first unofficial USDA evaluations based on SNP genotypes were released in April 2008. A steady increase in evaluation accuracy has resulted from including additional bulls with genotypes and traditional evaluations. Exchange of genotypes with other countries has increased the size of data sets to give more accurate genomic evaluations, and collaborations are expected to increase in the future.

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.