EuroGenomics
EuroGenomics is a consortium established in 2009 by cooperative partners with the ambition of providing to dairy farmers the most accurate and adapted tools, for an increased genetic progress and for a better farm management. Seven partners in the field of Holstein cattle breeding have therefore decided to join their forces:
- CRV, breeding company in the Netherlands,
- DHV, the Holstein breeder federation, and vit, their calculation center, in Germany,
- UNCEIA, the union of breeding companies in France,
- Viking Genetics, breeding company in the Nordic countries,
- CONAFE, the Holstein breeder federation, in Spain,
- and PFHBPM, union of the cattle breeder federation and the AI centres, in Poland.
The collaboration started with the share of genotypes (Holstein proven bulls) to build a very large reference population at the European level and therefore significantly increase the accuracy of the genomic selection in Holstein cattle. Today, EuroGenomics is managing the largest database of Holstein genotypes and phenotypes in the world. About 30,000 proven bulls are now contributing to the genomic predictions for male and female candidates of the various breeding schemes implemented in the 9 countries of the consortium.
However, to make the highest benefit of this large and unique database, EuroGenomics has to face with the heterogeneity of the tools and methods used by the different partners to generate genotypes and phenotypes.
(1) Heterogeneity of the genotyping chips: one of the first achievement of the consortium was the development of an imputation method to be able to benefit from the genomic information whatever the genotyping chip which was used (customized chips versus standard 50k chip of Illumina). Such development is the result of a strong scientific collaboration between the associated research units. This was of high interest as it was extended to impute missing markers from low density chips in order to increase the size of the genotyped population at a lower cost. Not only breeding companies benefited from a larger number of candidates but also farmers were provided by decisions tools for a finer management of the herd renewal and the matings. To go further, EuroGenomics encouraged a wider use of low density chips by developing a customized product, the EuroG10k dedicated to better manage genetic diseases and other genetic characteristics while participating to increase the accuracy of the genomic selection. This low density chips is regularly updated to integrate the more recent results on sequences, shared by the EuroGenomics partners and the associated research partners. To face with the heterogeneity of methods, the joint effort of EuroGenomics leading to more affordable tools, not only benefited to the Holstein population but also to the other dairy breeds managed by the various partners of the consortium.
(2) Heterogeneity of the phenotypes: the phenotypes that are required for the calibration of the genomic predictions are derived from data collected locally and analysed according to model and scale that differ from one country to another. Calculation centres are routinely using the international evaluations (Interbull) to express the breeding value estimates on the relevant scale and to provide the EuroGenomics partners with phenotypes for all proven bulls of the database. However, due to the “conversion step”, there are some loss of information that EuroGenomics would like to reduce. The associated calculation centres are now investing time to better harmonize the models of data analyses for traits routinely evaluated but also for traits under development. This is a great opportunity to benefit from the experience of a scientific network while continuing to account for the local specificities. This is a great opportunity to work all in the same direction, especially on the new traits, like health traits, that reinforce the image of the European cattle genetics towards sustainability.
When EuroGenomics initially shared genotypes of proven bull, it gave to all partners together the opportunity to achieve a critical size for a more affordable and more accurate genomic selection. In fact, such an experience with the reference population increased the range of data to be exchanged. Breeding companies are now sharing genotyping data on various types of animals (candidates, marketed young bulls). These data can be relevant for breeding scheme management (bilateral exchanges) or for a higher visibility of the partners on the international scene.
Finally, the EuroGenomics consortium facilitated the exchange of, not only data, but also idea. The close connection of the AI industry with the research units of various countries led to innovative tools like software and customized chips. In spite of the big contrasts between countries (size of the dairy population, type of structure, link between R&D and the industry, national priorities), the collaboration resulted in a more visible network, of scientific and professional forces, so that EuroGenomics is now recognized by international organizations. And such an effort made also the EuroGenomics countries more visible and attractive for export.
Farm animal breeders, including dairy cattle farmers have to face a large range of societal challenges in addition of the technical and economical issues. This is the role of EuroGenomics to keep facilitating innovation, so that each partner remain competitive while providing to the dairy farmers the best genetics.
- CRV, breeding company in the Netherlands,
- DHV, the Holstein breeder federation, and vit, their calculation center, in Germany,
- UNCEIA, the union of breeding companies in France,
- Viking Genetics, breeding company in the Nordic countries,
- CONAFE, the Holstein breeder federation, in Spain,
- and PFHBPM, union of the cattle breeder federation and the AI centres, in Poland.
The collaboration started with the share of genotypes (Holstein proven bulls) to build a very large reference population at the European level and therefore significantly increase the accuracy of the genomic selection in Holstein cattle. Today, EuroGenomics is managing the largest database of Holstein genotypes and phenotypes in the world. About 30,000 proven bulls are now contributing to the genomic predictions for male and female candidates of the various breeding schemes implemented in the 9 countries of the consortium.
However, to make the highest benefit of this large and unique database, EuroGenomics has to face with the heterogeneity of the tools and methods used by the different partners to generate genotypes and phenotypes.
(1) Heterogeneity of the genotyping chips: one of the first achievement of the consortium was the development of an imputation method to be able to benefit from the genomic information whatever the genotyping chip which was used (customized chips versus standard 50k chip of Illumina). Such development is the result of a strong scientific collaboration between the associated research units. This was of high interest as it was extended to impute missing markers from low density chips in order to increase the size of the genotyped population at a lower cost. Not only breeding companies benefited from a larger number of candidates but also farmers were provided by decisions tools for a finer management of the herd renewal and the matings. To go further, EuroGenomics encouraged a wider use of low density chips by developing a customized product, the EuroG10k dedicated to better manage genetic diseases and other genetic characteristics while participating to increase the accuracy of the genomic selection. This low density chips is regularly updated to integrate the more recent results on sequences, shared by the EuroGenomics partners and the associated research partners. To face with the heterogeneity of methods, the joint effort of EuroGenomics leading to more affordable tools, not only benefited to the Holstein population but also to the other dairy breeds managed by the various partners of the consortium.
(2) Heterogeneity of the phenotypes: the phenotypes that are required for the calibration of the genomic predictions are derived from data collected locally and analysed according to model and scale that differ from one country to another. Calculation centres are routinely using the international evaluations (Interbull) to express the breeding value estimates on the relevant scale and to provide the EuroGenomics partners with phenotypes for all proven bulls of the database. However, due to the “conversion step”, there are some loss of information that EuroGenomics would like to reduce. The associated calculation centres are now investing time to better harmonize the models of data analyses for traits routinely evaluated but also for traits under development. This is a great opportunity to benefit from the experience of a scientific network while continuing to account for the local specificities. This is a great opportunity to work all in the same direction, especially on the new traits, like health traits, that reinforce the image of the European cattle genetics towards sustainability.
When EuroGenomics initially shared genotypes of proven bull, it gave to all partners together the opportunity to achieve a critical size for a more affordable and more accurate genomic selection. In fact, such an experience with the reference population increased the range of data to be exchanged. Breeding companies are now sharing genotyping data on various types of animals (candidates, marketed young bulls). These data can be relevant for breeding scheme management (bilateral exchanges) or for a higher visibility of the partners on the international scene.
Finally, the EuroGenomics consortium facilitated the exchange of, not only data, but also idea. The close connection of the AI industry with the research units of various countries led to innovative tools like software and customized chips. In spite of the big contrasts between countries (size of the dairy population, type of structure, link between R&D and the industry, national priorities), the collaboration resulted in a more visible network, of scientific and professional forces, so that EuroGenomics is now recognized by international organizations. And such an effort made also the EuroGenomics countries more visible and attractive for export.
Farm animal breeders, including dairy cattle farmers have to face a large range of societal challenges in addition of the technical and economical issues. This is the role of EuroGenomics to keep facilitating innovation, so that each partner remain competitive while providing to the dairy farmers the best genetics.