Best Prediction of the Additive Genomic Variance in Random-Effects Models

ABSTRACT The additive genomic variance in linear models with random marker effects can be defined as a random variable that is in accordance with classical quantitative genetics theory. Common approaches to estimate the genomic variance in random-effects linear models based on genomic marker data can be regarded as the unconditional (or prior) expectation of this random additive genomic variance, and result in a negligence of the contribution of linkage disequilibrium. We introduce a novel best prediction (BP) approach for the additive genomic variance in both the current and the base population in the framework of genomic prediction using the gBLUP-method. The resulting best predictor is the conditional (or posterior) expectation of the additive genomic variance when using the additional information given by the phenotypic data, and is structurally in accordance with the genomic equivalent of the classical additive genetic variance in random-effects models. In particular, the best predictor includes the contribution of (marker) linkage disequilibrium to the additive genomic variance and eliminates the missing contribution of LD that is caused by the assumptions of statistical frameworks such as the random-effects model. We derive an empirical best predictor (eBP) and compare its performance with common approaches to estimate the additive genomic variance in random-effects models on commonly used genomic datasets.