Translocations associated with colour-sidedness are common in northern Swedish cattle breeds

The Swedish Mountain cattle and four other native Swedish cattle breeds show the phenotype of colour-sidedness. The causes of this phenotype are either a translocation and duplication from chromosome 6 to chromosome 29 (known as Cs₂₉) including the KIT gene, or an additional translocation allele where part of Cs₂₉ has been translocated back to chromosome 6 (Cs₆). Besides the colour-sidedness, the Cs₂₉ translocation has been associated with gonadal hypoplasia which can cause fertility problems. Despite breeding efforts during more than 80 years to reduce the prevalence of gonadal hypoplasia, there are still individuals with gonadal hypoplasia. We genotyped the Cs₂₉ and Cs₆ alleles in Swedish Mountain cattle and five other Swedish native breeds. Whole-genome sequence data of 30 cattle were analysed for the translocations, and 115 DNA samples were analysed using multiplex PCR. The current allele frequency of the Cs₂₉ allele in Swedish mountain cattle was estimated to be 44%. The results indicate that the Cs₂₉ translocation is also present in the four other native Swedish cattle breeds with colour-sidedness, and the Cs₆ translocation in at least three of them.