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Single-step methods for genomic evaluation in pigs

Published online by Cambridge University Press:  05 April 2012

O. F. Christensen ,
P. Madsen ,
B. Nielsen ,
T. Ostersen  and
G. Su
O. F. Christensen*
Affiliation:
Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, PO BOX 50, DK-8830 Tjele, Denmark
P. Madsen
Affiliation:
Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, PO BOX 50, DK-8830 Tjele, Denmark
B. Nielsen
Affiliation:
Breeding and Genetics, Pig Research Centre, The Danish Agriculture & Food Council, Axeltorv 3, DK-1609 Copenhagen V, Denmark
T. Ostersen
Affiliation:
Breeding and Genetics, Pig Research Centre, The Danish Agriculture & Food Council, Axeltorv 3, DK-1609 Copenhagen V, Denmark
G. Su
Affiliation:
Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, PO BOX 50, DK-8830 Tjele, Denmark
*
†E-mail: OleF.Christensen@agrsci.dk
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Abstract

Genetic evaluation based on information from phenotypes, pedigree and markers can be implemented using a recently developed single-step method. In this paper we compare accuracies of predicted breeding values for daily gain and feed conversion ratio (FCR) in Danish Duroc pigs obtained from different versions of single-step methods, the traditional pedigree-based method and the genomic BLUP (GBLUP) method. In particular, we present a single-step method with an adjustment of the genomic relationship matrix so that it is compatible to the pedigree-based relationship matrix. Comparisons are made for both genotyped and non-genotyped animals and univariate and bivariate models. The results show that the three methods with marker information (two single-step methods and GBLUP) produce more accurate predictions of genotyped animals than the pedigree-based method. In addition, single-step methods provide more accurate predictions for non-genotyped animals. The results also show that the single-step method with adjusted genomic relationship matrix produce more accurate predictions than the original single-step method. Finally, the results for the bivariate analyses show a somewhat improved accuracy and reduced inflation of predictions for FCR for the two single-step methods compared with the univariate analyses. The conclusions are: first, the methods with marker information improve prediction compared with the pedigree-based method; second, a single-step method, contrary to GBLUP, provides improved predictions for all animals compared to the pedigree-based method; and third, a single-step method should be used with an adjustment of the genomic relationship matrix.

Keywords

breeding valuegenetic parametersgenomic selectionmixed model methodspigs
Type
Full Paper
Information
animal , Volume 6 , Issue 10 , October 2012 , pp. 1565 - 1571
Copyright
Copyright © The Animal Consortium 2012

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