Influence of Foreign Genotypes on Genomic Breeding Values of National Candidates in Brown Swiss

Abstract Text: By using principal component analyses and calculating Fst statistics we found indications for a moderate subdivision of the current Brown Swiss population. Motivated by these results we started an investigation where we extended a strictly national calibration set used in genomic prediction with foreign genotypes in a stepwise manner to assess the dimension and relevance of resulting changes in predictions for national candidates. National candidates were further divided into a set of national descent and a set of partly mixed ancestry and differences between both groups were investigated. Results of this pilot study indicate that changes in genomic breeding values by augmenting the calibration group might be substantial. There are differences observable between the two groups of candidates. The mechanisms causing these effects are still not fully understood although joining international calibration sets is a common practice in genomic selection.

Keywords: dairy cattle, genomic breeding values, population subdivision