International single-step evaluations for beef cattle
Researchers from Wageningen University & Research (WUR), Interbeef, and Interbull Centre developed international evaluations that include genomic information from multiple countries.
Genomic evaluations allow predicting animals’ genetic merit at an early age by using genomic information. In beef cattle, genomic evaluations are becoming increasingly adopted nationally. However, current international evaluations, which combine data from different countries in a joint evaluation, do not yet consider genomic information. Researchers from WUR, Interbeef, and Interbull Centre developed international evaluations that include genomic information from multiple countries. Their results were published in Genetics Selection Evolution.
National and international genomic evaluations
Genomic evaluations use individual-level DNA information (SNPs) to predict an animal’s genetic merit, i.e., its estimated breeding value (EBV). A reference population composed of animals genotyped at thousands of SNPs with an associated phenotype is used to estimate the effect of the SNPs on the phenotypes. Knowing the SNPs’ effect and the SNPs of a selection candidate, its EBV can be predicted without measuring its phenotype or that of its offspring. Accurate genomic predictions often require large and representative reference populations, which can be expensive and time-consuming to build and maintain. Moreover, building a reference population using only national resources can be challenging or even unfeasible with small livestock populations. In these situations, an international genomic evaluation in which genomic data from different countries are jointly analysed is appealing, especially when genomic predictions are performed within the same breed. Moreover, even with the availability of large reference populations at the national level, combining genomic data with that of other countries could still be beneficial. In beef cattle, genomic data is increasingly becoming available nationally. However, current international beef cattle evaluations led by Interbeef are pedigree-based, i.e., they do not yet consider genomic information.
Benefits of international single-step genomic evaluations
Researchers developed a joint international single-step genomic evaluation for beef cattle using over 330,000 Limousin weaning weights from seven European countries and more than 17,000 genotyped animals. Single-step genomic evaluations are a state-of-the-art statistical methodology that analyse pedigree, phenotypic and genomic information in a single analysis. The authors investigated the benefits of implementing single-step evaluations by evaluating the increase in both the accuracies of EBVs and genetic connectedness among countries. They compared the new international single-step evaluations with current pedigree-based international evaluations and national evaluations (either pedigree-based or genomic). Additionally, researchers evaluated whether moving towards single-step evaluations would affect the bias of the EBVs. International single-step evaluations were beneficial for both large and small countries leading to higher population accuracies compared to current pedigree-based international evaluations and national evaluations. These increases are likely related to the larger multi-country reference population and the inclusion of phenotypes from relatives recorded in other countries achieved with the single-step international evaluation. Finally, single-step international evaluations gave similar or slightly reduced bias of EBVs compared to current pedigree-based evaluations. “In the context of international evaluations, the proposed single-step approach is novel because it uses raw phenotypic and genomic data from participating countries instead of approximating them as in other international evaluations” says Renzo Bonifazi, first author of the paper and researcher at the Animal Breeding and Genomics group. Given the increasing availability of genomic information at the national level and the increases in accuracies observed in the study, the implementation of international single-step evaluations in Interbeef should be considered in the near future.
Interbeef is a working group of ICAR (International Committee for Animal Recording) that aims to develop and promote national and international evaluations of beef cattle. Farmers seek to use the best bulls available to genetically improve their herds. The international organization called “Interbeef” has offered third-party international evaluations for beef cattle since 2006 and allows to compare national and foreign sires by computing international EBVs. Interbeef evaluations enable farmers to choose from a larger panel of elite bulls to better meet their selection objectives. Interbeef collaborates with fifteen countries worldwide, delivering genetic evaluations for five different breeds (Limousin, Charolais, Hereford, Simmental, and Angus) and three traits (weaning weight, calving ease, and birth weight).
The research described in this thesis was financially supported by the Interbeef Working Group, the International Committee for Animal Recording—ICAR (Rome, Italy), the International Bull Evaluation Service (Uppsala, Sweden), and the Irish Cattle Breeding Federation (ICBF, Link Road, Ballincollig, Co. Cork, Ireland).