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Reliabilities of genomic estimated breeding values in Danish Jersey

Published online by Cambridge University Press:  11 November 2011

J. R. Thomasen ,
B. Guldbrandtsen ,
G. Su ,
R. F. Brøndum  and
M. S. Lund
J. R. Thomasen*
Affiliation:
Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, PO Box 50, 8830 Tjele, Denmark VikingGenetics, Ebeltoftvej 16, 8860 Assentoft, Denmark
B. Guldbrandtsen
Affiliation:
Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, PO Box 50, 8830 Tjele, Denmark
G. Su
Affiliation:
Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, PO Box 50, 8830 Tjele, Denmark
R. F. Brøndum
Affiliation:
Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, PO Box 50, 8830 Tjele, Denmark
M. S. Lund
Affiliation:
Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, PO Box 50, 8830 Tjele, Denmark
*
†E-mail: jrt@vikinggenetics.com
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Abstract

In order to optimize the use of genomic selection in breeding plans, it is essential to have reliable estimates of the genomic breeding values. This study investigated reliabilities of direct genomic values (DGVs) in the Jersey population estimated by three different methods. The validation methods were (i) fivefold cross-validation and (ii) validation on the most recent 3 years of bulls. The reliability of DGV was assessed using squared correlations between DGV and deregressed proofs (DRPs). In the recent 3-year validation model, estimated reliabilities were also used to assess the reliabilities of DGV. The data set consisted of 1003 Danish Jersey bulls with conventional estimated breeding values (EBVs) for 14 different traits included in the Nordic selection index. The bulls were genotyped for Single-nucleotide polymorphism (SNP) markers using the Illumina 54 K chip. A Bayesian method was used to estimate the SNP marker effects. The corrected squared correlations between DGV and DRP were on average across all traits 0.04 higher than the squared correlation between DRP and the pedigree index. This shows that there is a gain in accuracy due to incorporation of marker information compared with parent index pre-selection only. Averaged across traits, the estimates of reliability of DGVs ranged from 0.20 for validation on the most recent 3 years of bulls and up to 0.42 for expected reliabilities. Reliabilities from the cross-validation were on average 0.24. For the individual traits, the reliability varied from 0.12 (direct birth) to 0.39 (milk). Bulls whose sires were included in the reference group had an average reliability of 0.25, whereas the bulls whose sires were not included in the reference group had an average reliability that was 0.05 lower.

Keywords

cross-validationdirect genomic valuegenomic selectionreliabilitycomposite breed
Type
Full Paper
Information
animal , Volume 6 , Special Issue 5: Symposium “Sustainable animal production in the tropics” (SAPT), Guadeloupe, France, November 15–18, 2010 , May 2012 , pp. 789 - 796
Copyright
Copyright © The Animal Consortium 2011

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