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United States Department of Agriculture

Agricultural Research Service

Title: Estimation of the Proportion of Variation Accounted for by DNA Tests. I: Genetic Variance

item Hanford, Kathryn
item Thallman, Richard - Mark
item Kachman, Stephen
item Kuehn, Larry
item Quaas, Richard
item Tempelman, Richard
item Fernando, Rohan
item Pollak, Emil

Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: 5/9/2010
Publication Date: 8/6/2010
Citation: Hanford, K.J., Thallman, R.M., Kachman, S.D., Kuehn, L.A., Quaas, R.L., Tempelman, R.J., Fernando, R.L., Pollak, E.J. 2010. Estimation of the Proportion of Variation Accounted for by DNA Tests. I: Genetic Variance. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany. August 1-6, 2010. CD-ROM Communication No. 0822.

Interpretive Summary: An increasingly relevant question in evaluating commercial DNA tests is "What proportion of the additive genetic variation in the target trait is accounted for by the test?" Therefore, two estimators of this quantity were evaluated by simulation of a population of 1000 animals with 100 sires, each with 10 progeny. One estimator was derived from a model including the target trait and the molecular breeding value (MBV) as a second trait. The MBV is a numerical value derived from the DNA test that predicts the additive genetic merit of an animal. The second estimator was derived from single trait models for the target trait, with or without, the MBV in the model. The estimator based on the two trait model performed better and is recommended for use in the independent validation of DNA tests.

Technical Abstract: The proportion of genetic variation accounted for (Rg2) is an important characteristic of a DNA test. For each of 3 levels of narrow sense heritability of the observed trait (h2gy) and 4 levels of Rg2, 500 independent replicates of an observed trait and a molecular breeding value (MBV) for 1000 offspring from 98-100 sires were simulated. For each of the same 12 combinations, an additional 500 replicates with non-additive genetic effects were generated so that the narrow sense heritability of MBV (h2gm) was equal to 0.8. The square of the genetic correlation from a multiple trait (MT) animal model with the MBV and observed phenotype included as correlated traits can be used to estimate Rg2. The reduction in sire variance (RV) between single trait sire models with and without the MBV covariate is an alternative estimator of Rg2. The MT estimator of Rg2 appeared better than the RV estimator.

Last Modified: 10/18/2017
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