Population structure of U.S. Holsteins allows for a snapshot of allele frequency changes and family specific SNPs

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Genetic change occurs in the U.S. Holstein population through the heavy use of specific bulls for a relatively short period of time. By focusing on a specific time-period, we were able to group a high percentage of the descendants of several prominent bulls into five different clusters. The average Fst across clusters was 0.03. Comparison between clusters revealed a heterogeneous mixture of allele frequency changes with varying degrees of magnitude and direction. Non-parallel responses between families suggests alternative goals and/or non-additive gene action. SNP effects for the trait stature were estimated independently for the five clusters and used to predict additive breeding values (BV). Correlations of within-cluster BVs with BVs based upon all animals combined varied from 0.70 to 0.88. By stratifying a population into subpopulations, family specific SNPs can be identified and used to increase or maintain genetic diversity.

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