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

F.G. Colinet, J. Vandenplas, S. Vanderick, H. Hammami, R.R. Mota, A. Gillon, X. Hubin, C. Bertozzi, N. Gengler

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

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.
Original languageEnglish
Pages (from-to)898-905
JournalAnimal
Volume12
Issue number5
DOIs
Publication statusPublished - 1 May 2018

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genomics
breeding value
prediction
pedigree
bulls
hands
methodology
animals
body conformation
information sources
udders
artificial insemination
Belgium
dairy cattle
Sweden
milk production
Holstein
genotype

Keywords

  • Bayesian integration
  • dairy cattle
  • genomic evaluation
  • reliabilities

Cite this

Colinet, F. G., Vandenplas, J., Vanderick, S., Hammami, H., Mota, R. R., Gillon, A., ... Gengler, N. (2018). Bayesian single-step genomic evaluations combining local and foreign information in Walloon Holsteins. Animal, 12(5), 898-905. https://doi.org/10.1017/S1751731117002324
Colinet, F.G. ; Vandenplas, J. ; Vanderick, S. ; Hammami, H. ; Mota, R.R. ; Gillon, A. ; Hubin, X. ; Bertozzi, C. ; Gengler, N. / Bayesian single-step genomic evaluations combining local and foreign information in Walloon Holsteins. In: Animal. 2018 ; Vol. 12, No. 5. pp. 898-905.
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Colinet, FG, Vandenplas, J, Vanderick, S, Hammami, H, Mota, RR, Gillon, A, Hubin, X, Bertozzi, C & Gengler, N 2018, 'Bayesian single-step genomic evaluations combining local and foreign information in Walloon Holsteins', Animal, vol. 12, no. 5, pp. 898-905. https://doi.org/10.1017/S1751731117002324

Bayesian single-step genomic evaluations combining local and foreign information in Walloon Holsteins. / Colinet, F.G.; Vandenplas, J.; Vanderick, S.; Hammami, H.; Mota, R.R.; Gillon, A.; Hubin, X.; Bertozzi, C.; Gengler, N.

In: Animal, Vol. 12, No. 5, 01.05.2018, p. 898-905.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - Bayesian single-step genomic evaluations combining local and foreign information in Walloon Holsteins

AU - Colinet, F.G.

AU - Vandenplas, J.

AU - Vanderick, S.

AU - Hammami, H.

AU - Mota, R.R.

AU - Gillon, A.

AU - Hubin, X.

AU - Bertozzi, C.

AU - Gengler, N.

PY - 2018/5/1

Y1 - 2018/5/1

N2 - 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.

AB - 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.

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KW - dairy cattle

KW - genomic evaluation

KW - reliabilities

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DO - 10.1017/S1751731117002324

M3 - Article

VL - 12

SP - 898

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SN - 1751-7311

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