Development of a single-step genomic evaluation for udder support in a multi-breed population with crossbred animals
Abstract
In Swiss dairy cattle, pedigree-based breeding values are predicted for Holstein (HO), Swiss Fleckvieh (SF) and Simmental (SI) in a combined evaluation. Although Holstein and Simmental have no recent common genetic history this combined evaluation is possible and stable due to the link established by SF, a cross between HO and SI. The multi-breed evaluation allows higher EBV accuracies particularly for SI as this population is relatively small.
Development of a single-step evaluation for dairy cattle in Switzerland is currently in progress. Udder support is used as example trait. The current multi-breed and crossbred setup must be kept leveraging the benefits of improved accuracies of the combined evaluation. Multiple methods were presented to tackle the problems imposed by a single-step multi-breed evaluation. Using MiX99, a ssGTaBLUP approach was used with all phenotypic and genotypic data available for HO, SF, and SI animals. A residual polygenic term was included at 10% as well as genetic groups specific to each breed. All genotypes were imputed to a density of 125K SNP and reliabilities were estimated according to Ben Zaabza et al. (2020). Scenarios were compared that included phenotypes and genotypes of only one breed or of different combinations of breeds. The aim of the different scenarios was to determine whether the genetic link provided by the crossbred animals could be correctly accounted for in our multi-breed evaluation. Results showed that single-step multi-breed evaluation led to less overestimation of candidate bulls EBV and lower EBV biases in all cases but for the exception of HO candidates. Further work will focus on this breed to improve its validation results.
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