Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 539454
Title Sparse single-step genomic blup in crossbreeding schemes
Author(s) Vandenplas, Jérémie; Calus, Mario P.L.; Napel, Jan ten
Source Journal of Animal Science 96 (2018)6. - ISSN 0021-8812 - p. 2060 - 2073.
DOI http://dx.doi.org/10.1093/jas/sky136
Department(s) LR - Animal Breeding & Genomics
WIAS
Animal Breeding and Genetics
Publication type Refereed Article in a scientific journal
Publication year 2018
Availibility Full text available from 2019-06-01
Keyword(s) APY - Genomic evaluation - Single-step
Abstract

The algorithm for proven and young animals (APY) efficiently computes an approximated inverse of the genomic relationship matrix, by dividing genotyped animals in the so-called core and noncore animals. The APY leads to computationally feasible single-step genomic Best Linear Unbiased Prediction (ssGBLUP) with a large number of genotyped animals and was successfully applied to real single-breed or line datasets. This study aimed to assess the quality of genomic estimated breeding values (GEBV) when using the APY (GEBVAPY), in comparison to GEBV when using the directly inverted genomic relationship matrix (GEBVDIRECT), for situations based on crossbreeding schemes, including F1 and F2 crosses, such as the ones for pigs and chickens. Based on simulations of a 3-way crossbreeding program, we compared different approximated inverses of a genomic relationship matrix, by varying the size and the composition of the core group. We showed that GEBVAPY were accurate approximations of GEBVDIRECT for multivariate ssGBLUP involving different breeds and their crosses. GEBVAPY as accurate as GEBVDIRECT were obtained when the core groups included animals from different breed compositions and when the core groups had a size between the numbers of the largest eigenvalues explaining 98% and 99% of the variation in the raw genomic relationship matrix.

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