Genetic evaluation including intermediate omics features

doi:10.1093/genetics/iyab130

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Genetic evaluation including intermediate omics features

2021-08-07

Ole Fredslund Christensen *

Vinzent Börner

L. Varona

Andrés Legarra

DOI：10.1093/genetics/iyab130

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Abstract

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In animal and plant breeding and genetics, there has been an increasing interest in intermediate omics traits, such as metabolomics and transcriptomics, which mediate the effect of genetics on the phenotype of interest. For inclusion of such intermediate traits into a genetic evaluation system, there is a need for a statistical model that integrates phenotypes, genotypes, pedigree, and omics traits, and a need for associated computational methods that provide estimated breeding values. In this paper, a joint model for phenotypes and omics data is presented, and a formula for the breeding values on individuals is derived. For complete omics data, three equivalent methods for best linear unbiased prediction of breeding values are presented. In all three cases, this requires solving two mixed model equation systems. Estimation of parameters using restricted maximum likelihood is also presented. For incomplete omics data, extensions of two of these methods are presented, where in both cases, the extension consists of extending an omics-related similarity matrix to incorporate individuals without omics data. The methods are illustrated using a simulated data set.

Keywords:

genetic evaluation

breeding value

mixed model equations

single-step method

transcriptomics

metabolomics

Genomic Prediction

GenPred

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