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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: Impact of adding foreign genomic information on Mexican Holstein imputation

Authors
item García-Ruiz, Adriana -
item Ruiz-Lopez, Felipe -
item Wiggans, George
item Van Tassell, Curtis
item Montaldo, Hugo -

Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: April 21, 2014
Publication Date: August 17, 2014
Citation: García-Ruiz, A., Ruiz-Lopez, F.J., Wiggans, G.R., Van Tassell, C.P., Montaldo, H. 2014. Impact of adding foreign genomic information on Mexican Holstein imputation. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.

Technical Abstract: The impact of adding US and Canada genomic information to the imputation of Mexican Holstein genotypes was measured by comparing 3 scenarios: 1) 2,018 Mexican genotyped animals; 2) animals from scenario 1 plus 886 related North American animals; and 3) animals from scenario 1 and all North American genotyped animals (338,073). Four different chip densities were imputed to 45,195 markers using findhap software. Imputation success was measured by comparing the number of half (HM) and completely missing (CM) SNP and conflicts. Imputation accuracy was improved when numbers of markers and genotyped animals were increased. The HM average was greater than the CM average for all scenarios. The largest number of conflicts was found between scenarios 1 and 3. The inclusion of genomic information of parents with daughters in the destination population improved imputation as did the inclusion of all available genotypes.

Last Modified: 9/22/2014
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