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

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. Wall...

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Bibliographic Details
Published in:Animal (Cambridge, England) England), 2018-05, Vol.12 (5), p.898-905
Main Authors: Colinet, F. G., Vandenplas, J., Vanderick, S., Hammami, H., Mota, R. R., Gillon, A., Hubin, X., Bertozzi, C., Gengler, N.
Format: Article
Language:English
Subjects:
Animal populations
Animal production & animal husbandry
Animals
Artificial insemination
Bayes Theorem
Bayesian analysis
Bayesian integration
Belgium
Bovidae
Breeding
Breeding and genetics
Cattle
Cattle - genetics
Counting
dairy cattle
Evaluation
Female
Genome - genetics
genomic evaluation
Genomics
Genotype
Genotypes
Information sources
Life sciences
Male
Mathematical models
Milk
Milk production
Pedigree
Phenotype
Populations
Productions animales & zootechnie
reliabilities
Reproduction (biology)
Research Article
Science
Sciences du vivant
Sweden
Udder
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Summary: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 (
ISSN:1751-7311
1751-732X
1751-732X
DOI:10.1017/S1751731117002324