A comparison of identity-by-descent and identity-by-state matrices that are used for genetic evaluation and estimation of variance components

Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie
Rohan L FernandoDorian J Garrick

Abstract

The genetic covariance matrix conditional on pedigree is proportional to the pedigree-based additive relationship matrix (PARM), which is twice the matrix of identity-by-descent (IBD) probabilities. In genomic prediction, IBD probabilities in the PARM, which are expected genetic similarities between relatives that are derived from the pedigree, are substituted by realized similarities that are derived from genotypes to obtain a genomic additive relationship matrix (GARM). Different definitions of similarity lead to different GARMs, and two commonly used GARMS are the matrix G, which is based on an allele substitution effect model, and the matrix T, which is based on an allele effect model. We show that although the two matrices T and G are not proportional, they give identical predictions of differences between breeding values. When genomic information is used for variance component estimation, the GARM Gx is computed from genotype covariates that have been standardized to have unit variance. That approach is equivalent to fitting a random regression model using the same standardized covariates. We show that under Hardy-Weinberg and linkage equilibria (LE) that the genetic variance is kσγ2, where σγ2 is the variance of a random...Continue Reading

References

Jul 1, 1997·Journal of Animal Science·A Nejati-JavaremiJ P Gibson
Oct 24, 2008·Journal of Dairy Science·P M VanRaden
Jul 22, 2009·Genetics·Daniel GianolaRohan Fernando
Jun 22, 2010·Nature Genetics·Jian YangPeter M Visscher
Sep 30, 2010·Nature Reviews. Genetics·Joseph E PowellMichael E Goddard
Jun 28, 2011·Genetics, Selection, Evolution : GSE·Ismo Strandén, Ole F Christensen
Nov 19, 2014·Nature Reviews. Genetics·Doug Speed, David J Balding
Apr 19, 2015·Genetics, Selection, Evolution : GSE·Sergio Vela-AvitúaJørgen Ødegård
May 6, 2015·PLoS Genetics·Gustavo de Los CamposDaniel Gianola
May 9, 2015·G3 : Genes - Genomes - Genetics·Hao ChengRohan Fernando

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Citations

Jul 10, 2019·The Journal of Heredity·Solomon BoisonNicholas Robinson
Jan 7, 2018·BMC Genetics·Ling-Yun ChangRomdhane Rekaya
Nov 26, 2019·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Leticia P SanglardNick V L Serão
Aug 7, 2019·Genetics·Nicholas SchreckMartin Schlather
Dec 13, 2019·Theoretical Population Biology·Daniel GianolaChris-Carolin Schön
Oct 1, 2019·Genetics·Nicholas SchreckMartin Schlather

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