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 SNP half (HM), completely missing (CM) 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 different SNP filled (conflicts) was found between scenarios 1 and 3. The inclusion of genomic information of parents with daughters in the destination population improved accuracy imputation as did the inclusion of all available genotypes.

Felipe J Ruiz-Lopez, Adriana García-Ruiz, George R Wiggans, Curt P VanTassell, Hugo H Montaldo

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Genetic Improvement Programs: Selection using molecular information (Posters), , 479, 2014
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