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Title: Imputation of Cow Genotypes and Adjustment of PTAs

Author
item Cooper, Tabatha
item Tooker, Melvin
item Vanraden, Paul
item Wiggans, George
item Cole, John

Submitted to: AIPL Research Reports
Publication Type: Government Publication
Publication Acceptance Date: 4/14/2010
Publication Date: 4/14/2010
Citation: Cooper, T.A., Tooker, M.E., Van Raden, P.M., Wiggans, G.R., Cole, J.B. 2010. Imputation of Cow Genotypes and Adjustment of PTAs. AIPL Research Reports. GENOMICS1 (4-10).

Interpretive Summary: The imputation of cow genotypes and the adjustment of cow predicted transmitting abilities (PTA) were added to the April 2010 genomic release. The imputation added 1600 cow genotypes to the database for Holstein, Jersey and Brown Swiss. The cow adjustment affected cows through the direct adjustment of their PTA and the adjustment made to the maternal portion of the parent average (PA). Bulls were only affected by the adjustment of the PA. Both implementations increased the accuracy of the genomic evaluations.

Technical Abstract: Two new techniques were introduced in April 2010 to incorporate all available information in the evaluations. The use of imputed genotypes has added over 1600 cows to the genomic database, and adjusting cow evaluations has increased accuracy. All other countries that are producing genomic evaluations do not use any cow information in genomic predictions. The US has made the decision to use cow information when it is available, rather than ignore the female contribution to the genomic equation. In order to do this, cow evaluations need to be similar to those of the bulls. Adjusting the cows increases the accuracy of the evaluations, and allows all the data available to be used in the genomic equations. The largest change occurs in the genotyped or imputed cows that have high reliability because their PTAs are less influenced by the parent average (PA), and receive larger adjustments. Big changes were also observed in popular bulls such as Shottle. These changes were due in part to how productive life is now calculated as well as the impact the adjustment had on bulls with a high number of genotyped daughters. Several specific examples of cows that had extreme drops in their PTAs have been hand inspected and the new PTAs are more closely related to the performance of their offspring.