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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #353407

Research Project: Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals

Location: Animal Genomics and Improvement Laboratory

Title: Pedigree verification and parentage assignment using genomic information in the Mexican Holstein population

Author
item GARCIA-RUIZ, ADRIANA - COLLABORATOR
item WIGGANS, GEORGE - RETIRED ARS EMPLOYEE
item RUIZ-LOPEZ, FELIPE - COLLABORATOR

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/22/2018
Publication Date: 2/1/2019
Citation: Garcia-Ruiz, A., Wiggans, G.R., Ruiz-Lopez, F.J. 2019. Pedigree verification and parentage assignment using genomic information in the Mexican Holstein population. Journal of Dairy Science. 102(2):1806–1810. https://doi.org/10.3168/jds.2018-15076.
DOI: https://doi.org/10.3168/jds.2018-15076

Interpretive Summary: Pedigree information is an essential tool to carry out any genetic improvement program. Pedigree verification and parent discovery for sires of cows, dams of cows, sires of bulls, and dams of bulls was conducted for the Mexican registered Holstein population using Mexican and U.S. Holstein ancestor genotypes. The percentage of paternal pedigree errors was around 10%, which is similar to the percentage reported for other Holstein populations. True parents were discovered for around 16% of Mexican animals with parentage conflicts. These results highlight the opportunity to improve pedigree accuracy and the rate of genetic gain through the implementation of a continuous parentage verification and discovery program using genomic information.

Technical Abstract: Pedigree information is an essential tool to carry out any genetic improvement program. The objective of this study was to determine the accuracy of pedigree information for the Mexican Holstein registered population using genomic data available in Mexico and the United States. Data from 7,508 animals registered with the Mexican Holstein Association (158 sires and 7,350 cows), born from 2002 through 2014, and genotyped with different SNP array densities were included in the study. For 17% of cow sires and 12% of bull sires included in the study, parentage could not be validated. Most of the cow and bull dams (79% for both sexes) had no genotype available and, therefore, could not be validated. Among the animals included in the analysis, a parentage test was possible only for 6,104 cow sires, 139 bull sires, 1,519 cow dams, and 33 bull dams, and these animals were considered to be the base for each source of information. Parentage was confirmed for 89% of cow sires, 92% of cow dams, 95% of bull sires, and 97% of bull dams. For animals with an unconfirmed parent, discovery was possible for 17% of cow sires, 2.5% of cow dams, 43% of bull sires, and no bull dams. Of the total 7,795 parentage tests, 777 were conflicts, which is a 9.97% rate for paternity recording mistakes in the population and similar to rates recently found for other Holstein populations. True parents were discovered for around 16% of Mexican animals with parentage conflicts; parents were considered to be missing for the remaining animals with parentage conflicts. This study will help improve rates of genetic gain and indicates that genotyping should continue to ensure the improvement of future generations.