This study aimed to investigate the use of genomic information in combination with real data at quantitative and qualitative levels in the framework of the current national genetic evaluation scheme for the Slovenian Brown Swiss cattle population. We investigated the possibility of introducing a national genomic evaluation with a small national cow-based reference population and integrating external and genomic information of foreign bulls. We showed that incorporating a large amount of foreign genomic and external information into national genomic evaluation results in the highest reliability of estimated genomic breeding values and less biased estimated genomic breeding values. That way, young selection candidates obtain the same or more reliable estimated genomic breeding values much earlier than in a conventional genetic evaluation scheme. By using (improved) national rather than international estimated genomic breeding values, a more comprehensive re-ranking for production traits is possible. We also investigated the effect of selection that considers favourable alleles of beneficial Mendelian traits on genetic improvement at the herd level. We have shown that selection for a favourable genotype of a beneficial Mendelian trait can have a negative impact on the genetic improvement of quantitative traits, with the magnitude of the response to selection depending on the existing selection pressure and the interaction between the specific Mendelian and quantitative traits at the herd level. The results of this study can be used to advance the routine national dairy cattle evaluation scheme.
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