Epistasis and covariance: how gene interaction translates into genomic relationship

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Johannes W R MartiniHenner Simianer

Abstract

Models based on additive marker effects and on epistatic interactions can be translated into genomic relationship models. This equivalence allows to perform predictions based on complex gene interaction models and reduces computational effort significantly. In the theory of genome-assisted prediction, the equivalence of a linear model based on independent and identically normally distributed marker effects and a model based on multivariate Gaussian distributed breeding values with genomic relationship as covariance matrix is well known. In this work, we demonstrate equivalences of marker effect models incorporating epistatic interactions and corresponding mixed models based on relationship matrices and show how to exploit these equivalences computationally for genome-assisted prediction. In particular, we show how models with epistatic interactions of higher order (e.g., three-factor interactions) translate into linear models with certain covariance matrices and demonstrate how to construct epistatic relationship matrices for the linear mixed model, if we restrict the model to interactions defined a priori. We illustrate the practical relevance of our results with a publicly available data set on grain yield of wheat lines grow...Continue Reading

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Citations

Jun 26, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Matthias WesthuesAlbrecht E Melchinger
Jan 27, 2019·Genetics·Nicholas SantantonioMark Sorrells
Jan 19, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Matthias WesthuesAlbrecht E Melchinger
Jul 28, 2020·G3 : Genes - Genomes - Genetics·Matías F SchraufSebastián Munilla
Dec 13, 2016·BMC Genomics·Marcio Balestre, Claudio Lopes de Souza
Mar 22, 2018·Frontiers in Genetics·Luis VaronaZulma G Vitezica
Feb 19, 2019·Plant Methods·Filipe Couto AlvesGustavo de Los Campos
Mar 13, 2019·Frontiers in Genetics·Zhengcao LiHenner Simianer
Mar 1, 2019·G3 : Genes - Genomes - Genetics·Nicholas SantantonioMark Sorrells
Mar 1, 2019·G3 : Genes - Genomes - Genetics·Nicholas SantantonioMark Sorrells
Apr 18, 2021·Genetics·David González-DiéguezZulma G Vitezica
Feb 15, 2019·G3 : Genes - Genomes - Genetics·Johannes W R MartiniThomas Kneib
Aug 5, 2016·G3 : Genes - Genomes - Genetics·Daniel Gianola, Chris-Carolin Schön
Apr 20, 2021·G3 : Genes - Genomes - Genetics·Jie ZhangYong Jiang
Jun 12, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Elaheh VojganiHenner Simianer
Jan 2, 2022·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Miguel Angel RaffoJust Jensen
Dec 3, 2021·Animal Genetics·P DavoodiA A Masoudi

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