Solving efficiently large single-step genomic best linear unbiased prediction models

Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie
I StrandénE A Mäntysaari

Abstract

Single-step genomic BLUP (ssGBLUP) requires a dense matrix of the size equal to the number of genotyped animals in the coefficient matrix of mixed model equations (MME). When the number of genotyped animals is high, solving time of MME will be dominated by this matrix. The matrix is the difference of two inverse relationship matrices: genomic (G) and pedigree (A22 ). Different approaches were used to ease computations, reduce computing time and improve numerical stability. Inverse of A22 can be computed as A22-1=A22-A21A11-1A12 where Aij , i, j = 1,2, are sparse sub-matrices of A-1 , and numbers 1 and 2 refer to non-genotyped and genotyped animals, respectively. Inversion of A11 was avoided by three alternative approaches: iteration on pedigree (IOP), matrix iteration in memory (IM), and Cholesky decomposition by CHOLMOD library (CM). For the inverse of G, the APY (algorithm for proven and young) approach using Cholesky decomposition was formulated. Different approaches to choose the APY core were compared. These approaches were tested on a joint genetic evaluation of the Nordic Holstein cattle for fertility traits and had 81,031 genotyped animals. Computing time per iteration was 1.19 min by regular ssGBLUP, 1.49 min by IOP, 1...Continue Reading

References

Jan 12, 2000·Journal of Dairy Science·I Strandén, M Lidauer
Jul 27, 2001·Journal of Dairy Science·W F Fikse, G Banos
Jun 8, 2004·Biometrics·Mary Sara McPeekCarole Ober
Oct 24, 2008·Journal of Dairy Science·P M VanRaden
Jan 29, 2010·Genetics, Selection, Evolution : GSE·Ole F Christensen, Mogens S Lund
Dec 10, 2013·Genetics, Selection, Evolution : GSE·Pierre Faux, Nicolas Gengler
Apr 1, 2014·Journal of Dairy Science·I MisztalI Aguilar
Jul 16, 2014·Journal of Dairy Science·Z LiuR Reents
Sep 26, 2014·Genetics, Selection, Evolution : GSE·Rohan L FernandoDorian J Garrick
Feb 11, 2015·Journal of Dairy Science·M KoivulaE A Mäntysaari

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Citations

Feb 28, 2018·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·M KoivulaE A Mäntysaari
Aug 17, 2018·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Kaarina MatilainenEsa A Mäntysaari
Nov 14, 2018·Journal of Animal Science·Elizabeth M van GrevenhofMario P L Calus
Nov 26, 2018·Journal of Dairy Science·M N AldridgeM P L Calus
Apr 9, 2020·Journal of Animal Science·Ignacy MisztalAndres Legarra
Aug 5, 2018·Genetics, Selection, Evolution : GSE·Karin MeyerAndrew Swan
Feb 23, 2020·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Ignacio AguilarAndres Legarra
Jun 7, 2018·Journal of Animal Science·Jérémie VandenplasJan Ten Napel
May 19, 2020·Journal of Dairy Science·A A KudinovI Strandén
Apr 26, 2020·Journal of Dairy Science·E A MäntysaariI Strandén
Jan 26, 2021·Journal of Animal Science·Yutaka MasudaIgnacy Misztal
Mar 7, 2021·Animals : an Open Access Journal From MDPI·Miguel A Gutierrez-ReinosoManuel Garcia-Herreros

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