Orthogonal Estimates of Variances for Additive, Dominance, and Epistatic Effects in Populations

Genetics
Zulma G VitezicaLuis Varona

Abstract

Genomic prediction methods based on multiple markers have potential to include nonadditive effects in prediction and analysis of complex traits. However, most developments assume a Hardy-Weinberg equilibrium (HWE). Statistical approaches for genomic selection that account for dominance and epistasis in a general context, without assuming HWE (e.g., crosses or homozygous lines), are therefore needed. Our method expands the natural and orthogonal interactions (NOIA) approach, which builds incidence matrices based on genotypic (not allelic) frequencies, to include genome-wide epistasis for an arbitrary number of interacting loci in a genomic evaluation context. This results in an orthogonal partition of the variances, which is not warranted otherwise. We also present the partition of variance as a function of genotypic values and frequencies following Cockerham's orthogonal contrast approach. Then we prove for the first time that, even not in HWE, the multiple-loci NOIA method is equivalent to construct epistatic genomic relationship matrices for higher-order interactions using Hadamard products of additive and dominant genomic orthogonal relationships. A standardization based on the trace of the relationship matrices is, however,...Continue Reading

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Citations

Jul 23, 2018·Journal of Animal Science·Fernanda S S RaidanAntonio Reverter
Nov 2, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Danilo Hottis LyraRoberto Fritsche-Neto
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