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United States Department of Agriculture

Agricultural Research Service

Research Project: Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information

Location: Animal Genomics and Improvement Laboratory

Title: Calculation and delivery of US genomic evaluations for dairy cattle

Authors
item Wiggans, George
item Cooper, Tabatha
item Vanraden, Paul
item Null, Daniel
item Hutchison, Jana
item Meland, Ole -
item Tooker, Melvin
item Norman, Howard -

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: March 22, 2014
Publication Date: July 20, 2014
Citation: Wiggans, G.R., Cooper, T.A., Van Raden, P.M., Null, D.J., Hutchison, J.L., Meland, O.M., Tooker, M.E., Norman, H.D. 2014. Calculation and delivery of US genomic evaluations for dairy cattle. Journal of Dairy Science. 97(E-Suppl. 1):77–78 (abstr. 0152).

Technical Abstract: In April 2013, the responsibility for calculation and distribution of genomic evaluations for dairy cattle was transferred from the USDA to the US dairy industry’s Council on Dairy Cattle Breeding; the responsibility for development of evaluation methodology remained with the USDA. The Council on Dairy Cattle Breeding has implemented a fee schedule to provide operational funds as well as an incentive for continued submission of phenotypic data necessary for estimation of genomic effects. Since April 2013, substantial improvements have been made to the evaluation system. The number of SNP used for all evaluations has been increased to 61,013 from 45,195. The Jersey reference population has been increased by 1,186 Danish bull genotypes obtained through an exchange with Viking Genetics International (Skara, Sweden). Genomic evaluations for Ayrshires were released to the industry. Cutoff studies to assess the accuracy of data available 4 yr earlier for predicting current data showed the mean gain in reliability across traits for Holsteins was 0.5 percentage points from adding 15,818 SNP, 1.2 percentage points for adding the Jersey bulls, and 8.2 percentage points over parent average for Ayrshires. The weighting for cow evaluations used to estimate SNP effects has been reduced; the most recent adjustment was to prevent the evaluations of bulls with a high proportion of genotyped daughters from being distorted by the shrinkage of cow evaluations toward birth year means that are applied after the BLUP evaluations are calculated. Adjustment of cow weights improved the regression of genomic evaluation on future performance and reduced bias along with correcting anomalies in evaluations of high-reliability bulls. Multitrait traditional evaluations for heifer and cow conception rates are used to estimate SNP effects for those traits. Imputed values are now provided for gene tests for bovine leucocyte adhesion deficiency, complex vertebral malformation, deficiency of uridine monophosphate synthase, syndactyly, Weaver Syndrome, spinal dismyelination, spinal muscular atrophy, red coat color, and polledness. Four tests for haplotypes that affect fertility or stillbirth rate were added (HH4 and HH5 for Holsteins, BH2 for Brown Swiss, and AH1 for Ayrshires). As of January 2014, over 525,000 genotypes are used in genomic evaluation with a mean of 18,000 added monthly. Genomic evaluations are released for animals from 36 countries, an indication of the global demand for them.

Last Modified: 10/1/2014
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