Genomic prediction when some animals are not genotyped.

Genetics, Selection, Evolution : GSE
Ole F Christensen, M S Lund

Abstract

The use of genomic selection in breeding programs may increase the rate of genetic improvement, reduce the generation time, and provide higher accuracy of estimated breeding values (EBVs). A number of different methods have been developed for genomic prediction of breeding values, but many of them assume that all animals have been genotyped. In practice, not all animals are genotyped, and the methods have to be adapted to this situation. In this paper we provide an extension of a linear mixed model method for genomic prediction to the situation with non-genotyped animals. The model specifies that a breeding value is the sum of a genomic and a polygenic genetic random effect, where genomic genetic random effects are correlated with a genomic relationship matrix constructed from markers and the polygenic genetic random effects are correlated with the usual relationship matrix. The extension of the model to non-genotyped animals is made by using the pedigree to derive an extension of the genomic relationship matrix to non-genotyped animals. As a result, in the extended model the estimated breeding values are obtained by blending the information used to compute traditional EBVs and the information used to compute purely genomic EBV...Continue Reading

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Citations

Dec 15, 2010·Genetics Research·Andrés LegarraSébastien Fritz
Jul 20, 2011·Genetics Research·Z G VitezicaA Legarra
Jun 22, 2012·Animal : an International Journal of Animal Bioscience·O F ChristensenG Su
Jun 28, 2011·Genetics, Selection, Evolution : GSE·Ismo Strandén, Ole F Christensen
Jul 14, 2011·Genetics, Selection, Evolution : GSE·Miguel Angel ToroAndrés Legarra
Aug 20, 2011·Genetics, Selection, Evolution : GSE·Clotilde Patry, Vincent Ducrocq
Apr 24, 2012·Genetics, Selection, Evolution : GSE·Pooja GuptaKaspar Bienefeld
May 10, 2012·Genetics, Selection, Evolution : GSE·Jørgen Ødegård, Theo H E Meuwissen
Apr 3, 2012·Genetics, Selection, Evolution : GSE·John M HickeyMatthew A Cleveland
Oct 17, 2013·Genetics, Selection, Evolution : GSE·Thierry TriboutFlorence Phocas
Jun 8, 2011·BMC Proceedings·Fanny CalengeCatherine Beaumont
Jun 30, 2012·Genetics·Gustavo de Los CamposMario P L Calus
Dec 10, 2013·Genetics, Selection, Evolution : GSE·Pierre Faux, Nicolas Gengler
Mar 29, 2014·Genetics, Selection, Evolution : GSE·Ole F ChristensenGuosheng Su
Apr 18, 2014·Animal : an International Journal of Animal Bioscience·G E PollottD C Wathes
Aug 28, 2014·Genetics, Selection, Evolution : GSE·Xijiang YuTheo H E Meuwissen
Sep 26, 2014·Genetics, Selection, Evolution : GSE·Rohan L FernandoDorian J Garrick
Jan 22, 2013·Genetics·Xia ShenLars Rönnegård
Jan 3, 2016·Journal of Dairy Science·Z LiuR Reents
Oct 16, 2014·Genetics, Selection, Evolution : GSE·Xiujin LiXiangdong Ding
Jan 1, 2014·Genetics, Selection, Evolution : GSE·Jérémie VandenplasNicolas Gengler
Jan 20, 2016·Animal : an International Journal of Animal Bioscience·M S LundG Su
Apr 15, 2016·Animal : an International Journal of Animal Bioscience·M KoivulaE A Mäntysaari
Dec 24, 2015·Genetics, Selection, Evolution : GSE·Ole F ChristensenGuosheng Su
Dec 18, 2015·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·M S LopesH Bovenhuis
Sep 8, 2015·Journal of Dairy Science·S MuchaJ Conington
Nov 9, 2011·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·T H E MeuwissenJ A Woolliams
Jan 10, 2012·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·R SimeoneZ G Vitezica
Nov 9, 2011·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·I AguilarS Tsuruta
Jul 17, 2013·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·I MisztalA A Swan
Apr 11, 2015·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·B O FragomeniI Misztal

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Methods Mentioned

BETA
genotyping

Software Mentioned

REML
DMU
AI

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