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

Genetics
Nicholas SchreckMartin Schlather

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 estimating the unconditional (or prior) expectation of this random additive genomic variance, and result in a negligence of the contribution of linkage disequilibrium (LD). 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 genomic best linear unbiased prediction (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) LD to the additive genomic variance and possibly fully eliminates the missing contribution of LD that is caused by the assumptions of statistical framewo...Continue Reading

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Software Mentioned

GCTA
eBLUP
BGLR
GREML
REML
package
R Development Core Team
R
gBLUP
sommer ”

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