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Impact of Adding Foreign Genomic Information on the Mexican Holstein Imputation Process

Monday, August 18, 2014
Posters (The Westin Bayshore)
Felipe J Ruiz-Lopez , Natl. Cent. for Research on Physiology and Animal Breeding INIFAP, Queretaro, Mexico
Adriana García-Ruiz , National Autonomous University of Mexico (UNAM), Mexico, DF, Mexico
George R. Wiggans , Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD
Curt P VanTassell , Bovine Functional Genomics Laboratory ARS-USDA, Beltsville, MD
Hugo H Montaldo , Universidad Nacional Autónoma de México, DF, Mexico
Abstract Text:

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.

Keywords:

Imputation

Genomics

Mexico-Holstein

See more of: Posters: Prediction using molecular information (Group 2)
See more of: Genetic Improvement Programs: Selection using molecular information
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