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Bayesian single-step genomic evaluations combining local and foreign information in Walloon Holsteins

Published online by Cambridge University Press:  16 October 2017

F. G. Colinet ,
J. Vandenplas ,
S. Vanderick ,
H. Hammami ,
R. R. Mota ,
A. Gillon ,
X. Hubin ,
C. Bertozzi  and
N. Gengler
F. G. Colinet
Affiliation:
TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium
J. Vandenplas
Affiliation:
TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium National Fund for Scientific Research, 1000 Brussels, Belgium
S. Vanderick
Affiliation:
TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium
H. Hammami
Affiliation:
TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium
R. R. Mota
Affiliation:
TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium
A. Gillon
Affiliation:
Research and Development Department, Walloon Breeding Association, 5590 Ciney, Belgium
X. Hubin
Affiliation:
Research and Development Department, Walloon Breeding Association, 5590 Ciney, Belgium
C. Bertozzi
Affiliation:
Research and Development Department, Walloon Breeding Association, 5590 Ciney, Belgium
N. Gengler*
Affiliation:
TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium
*
†E-mail: [email protected]
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Abstract

Most dairy cattle populations found in different countries around the world are small to medium sized and use many artificial insemination bulls imported from different foreign countries. The Walloon population in the southern part of Belgium is a good example for such a small-scale population. Wallonia has also a very active community of Holstein breeders requesting high level genetic evaluation services. Single-step Genomic BLUP (ssGBLUP) methods allow the simultaneous use of genomic, pedigree and phenotypic information and could reduce potential biases in the estimation of genomically enhanced breeding values (GEBV). Therefore, in the context of implementing a Walloon genomic evaluation system for Holsteins, it was considered as the best option. However, in contrast to multi-step genomic predictions, natively ssGBLUP will only use local phenotypic information and is unable to use directly important other sources of information coming from abroad, for example Multiple Across Country Evaluation (MACE) results as provided by the Interbull Center (Uppsala, Sweden). Therefore, we developed and implemented single-step Genomic Bayesian Prediction (ssGBayes), as an alternative method for the Walloon genomic evaluations. The ssGBayes method approximated the correct system of equations directly using estimated breeding values (EBV) and associated reliabilities (REL) without any explicit deregression step. In the Walloon genomic evaluation, local information refers to Walloon EBV and REL and foreign information refers to MACE EBV and associated REL. Combining simultaneously all available genotypes, pedigree, local and foreign information in an evaluation can be achieved but adding contributions to left-hand and right-hand sides subtracting double-counted contributions. Correct propagation of external information avoiding double counting of contributions due to relationships and due to records can be achieved. This ssGBayes method computed more accurate predictions for all types of animals. For example, for genotyped animals with low Walloon REL (<0.25) without MACE results but sired by genotyped bulls with MACE results, the average increase of REL for the studied traits was 0.38 points of which 0.08 points could be traced to the inclusion of MACE information. For other categories of genotyped animals, the contribution by MACE information was also high. The Walloon genomic evaluation system passed for the first time the Interbull GEBV tests for several traits in July 2013. Recent experiences reported here refer to its use in April 2016 for the routine genomic evaluations of milk production, udder health and type traits. Results showed that the proposed methodology should also be of interest for other, similar, populations.

Keywords

dairy cattleBayesian integrationgenomic evaluationreliabilities
Type
Research Article
Information
animal , Volume 12 , Issue 5 , May 2018 , pp. 898 - 905
Copyright
© The Animal Consortium 2017 

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Footnotes

b

Present address: Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700 AH Wageningen, The Netherlands.

a

These authors contributed equally to this work.

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