Genomic evaluation of both purebred and crossbred performances

Ole F Christensen,Per Madsen,Guosheng Su,Bjarne Nielsen

doi:10.1186/1297-9686-46-23

Ole F Christensen, Per Madsen + Show 2 more

Open Access

https://doi.org/10.1186/1297-9686-46-23

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Abstract

BackgroundFor a two-breed crossbreeding system, Wei and van der Werf presented a model for genetic evaluation using information from both purebred and crossbred animals. The model provides breeding values for both purebred and crossbred performances. Genomic evaluation incorporates marker genotypes into a genetic evaluation system. Among popular methods are the so-called single-step methods, in which marker genotypes are incorporated into a traditional animal model by using a combined relationship matrix that extends the marker-based relationship matrix to non-genotyped animals. However, a single-step method for genomic evaluation of both purebred and crossbred performances has not been developed yet.ResultsAn extension of the Wei and van der Werf model that incorporates genomic information is presented. The extension consists of four steps: (1) the Wei van der Werf model is reformulated using two partial relationship matrices for the two breeds; (2) marker-based partial relationship matrices are constructed; (3) marker-based partial relationship matrices are adjusted to be compatible to pedigree-based partial relationship matrices and (4) combined partial relationship matrices are constructed using information from both pedigree and marker genotypes. The extension of the Wei van der Werf model can be implemented using software that allows inverse covariance matrices in sparse format as input.ConclusionsA method for genomic evaluation of both purebred and crossbred performances was developed for a two-breed crossbreeding system. The method allows information from crossbred animals to be incorporated in a coherent manner for such crossbreeding systems.

Highlights

For a two-breed crossbreeding system, Wei and van der Werf presented a model for genetic evaluation using information from both purebred and crossbred animals
Genomic selection of purebreds for crossbred performance was proposed by Ibánez-Escriche et al [7] that used phenotypes on crossbreds only, and a genomic model with breed of origin specific allele substitution effects
The aim of this paper is to present an extension of the Wei van der Werf model that incorporates genomic information

Summary

Introduction

For a two-breed crossbreeding system, Wei and van der Werf presented a model for genetic evaluation using information from both purebred and crossbred animals. For a two-breed crossbreeding system, Wei and van der Werf (Appendix 2 in [1]) presented a model for genetic evaluation using information from both purebred and crossbred animals. The study included genomic data, it was less sophisticated than the Wei and van der Werf model [1] since each animal had only one breeding value and phenotype recordings in purebreds were not used. It assumed that all relevant animals were genotyped, which would not be a very likely scenario in practice

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