International genetic and genomic evaluations of beef cattle

Abstract

. International genetic and genomic evaluations of beef cattle.PhD thesis, Wageningen University, the Netherlands.In cattle, advancements in reproductive technologies such as artificial insemination allowed breeders to access the genetic material of superior bulls from foreign countries. However, animals' estimated breeding values (EBV) computed from different national evaluations are not directly comparable across countries due to differences in scales and genetic bases, trait and model definitions, and the possible presence of genotype-by-environment interactions. International evaluations account for such differences by jointly analysing all national data and modelling the same trait recorded in different countries as different correlated traits. The resulting international EBV (EBV INT ) facilitate the comparison of domestic and foreign sires and worldwide trading of their genetic material. This thesis aimed to improve and further develop methodologies for international beef cattle evaluations (Interbeef) by addressing various challenges, mainly related to: i) the estimation of across-country genetic correlations (r g ) and their impact on the EBV INT ; ii) the inclusion of national genomic information; and iii) the development of an official procedure for participating countries to integrate the distributed EBV INT back into their national evaluations. First, I showed that both large and small participating countries benefit from current Interbeef pedigree-based evaluations. Second, I showed the feasibility of estimating across-country r g using a multi-trait approach that simultaneously fits data from all countries and proposed data sub-setting strategies to improve computational time. Third, I showed that the current practice of assuming across-country direct-maternal r g to be 0 has limited impact on the EBV INT of animals of interest such as publishable sires, i.e., sires that meet Interbeef publications rules. On the other hand, assuming zero within-country direct-maternal r g impacts the EBV INT of such animals. Fourth, I developed international genomic evaluations for beef cattle using a single-step SNPBLUP approach (ssSNPBLUP). International ssSNPBLUP evaluations lead to higher accuracies compared to both current international pedigree evaluations and either national pedigree or genomic evaluations, while keeping similar or slightly reduced level and dispersion bias. Finally, I developed a generalized procedure to integrate pedigree-based or singlestep EBV INT of publishable sires into national evaluations. The procedure can be easily implemented with current software. Compared to national evaluations without integration, the integration reduces level bias, gives similar dispersion, and increases accuracies of publishable sires' EBV INT . Overall, this thesis contributes to the development of international evaluations of beef cattle.

Genetic Parameters for Limousine Interbeef Genetic Evaluation of Calving Traits

“…The estimation of across-country r g in beef cattle is challenging due to an usually lower level of genetic connectedness related to the lower usage of AI compared to dairy breeds like Holstein [11]. The number of common bulls presented in our study is consistent with those in previous studies [7,10,12,13,28]. Moreover, 55.4% (BWT) and 51.8% (CAE) of common bulls connected only two populations.…”

“…Genetic correlations (r g ) are key for international evaluations, as they determine how much the information about relatives recorded in one country affects the animal's international breeding value in another country [10]. The estimation of across-country r g in beef cattle is challenging due to the usually lower level of genetic connectedness, related to the lower usage of AI, compared to dairy breeds like Holstein [11] and the need to incorporate maternal genetic effects and maternal permanent environmental effects into the model [2,4].…”

Single‐step SNPBLUP evaluation in six German beef cattle breeds

“…Given that the inclusion of genomic records increases the relationship between animals by enabling the identification of alleles identical in state that can be shared through common ancestors that may not be recorded in the PBLUP approach, one may expect that the accuracy of the singlestep approach should be significantly higher compared to the PBLUP. However, in agreement with other studies in beef cattle (Bonifazi, 2022), this was not the case in our study. This is attributed to the lower connectedness and smaller sire families of the German beef cattle populations.…”