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This article in JAS

  1. Vol. 95 No. 4, p. 1472-1480
     
    Received: Oct 27, 2016
    Accepted: Feb 19, 2017
    Published: April 13, 2017


    2 Corresponding author(s): tao.xiang@mbg.au.dk
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doi:10.2527/jas.2016.1155

Technical note: Genomic evaluation for crossbred performance in a single-step approach with metafounders1

  1. T. Xiang 2*†,
  2. O. F. Christensen* and
  3. A. Legarra
  1. * Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830 Tjele, Denmark
     INRA, UR1388 GenPhyse, CS-52627, F-31326 Castanet-Tolosan, France

Abstract

A single-step genomic BLUP method (ssGBLUP) has been successfully developed and applied for purebred and crossbred performance in pigs. However, it requires phasing the genotypes and inferring the breed origin of alleles in crossbred animals, which is somewhat inconvenient. Recently, a new concept of metafounders that considers the relationship within and across base populations was developed. With this concept of metafounders, regular methods to build and invert the pedigree relationships matrix can be used with only minor modifications and, moreover, genomic relationships and pedigree-based relationships are automatically compatible in the ssGBLUP. In this study, data for the total number of piglets born in Danish Landrace, Yorkshire, and 2-way crossbred pigs and models for purebred and crossbred performance were revisited by use of ssGBLUP with 2 metafounders. Genetic variances and genetic correlations between purebred and crossbred performances were first reestimated. Then, model-based reliabilities of purebred boars for their crossbred performance and predictive abilities for crossbred animals were compared in different scenarios. Results in this study were compared to those in a previous study with identical data but with models that required known breed origin of crossbred genotypes. Results show that relationships for base individuals within Landrace and within Yorkshire are similar and that the ancestor populations for Landrace and Yorkshire are related. In terms of model-based reliabilities and predictive abilities, ssGBLUP with metafounders performs at least as well as the single-step method requiring phasing at a lower complexity.

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