A non‐coding regulatory variant in the 5′‐region of the MITF gene is associated with white‐spotted coat in Brown Swiss cattle

Summary Recently, the Swiss breeding association reported an increasing number of white‐spotted cattle in the Brown Swiss breed, which is normally solid brown coloured. A total of 60 Brown Swiss cattle with variably sized white abdominal spots, facial markings and depigmented claws were collected for this study. A genome‐wide association study using 40k SNP genotypes of 20 cases and 1619 controls enabled us to identify an associated genome region on chromosome 22 containing the MITF gene, encoding the melanogenesis associated transcription factor. Variants at the MITF locus have been reported before to be associated with white or white‐spotted phenotypes in other species such as horses, dogs and mice. Whole‐genome sequencing of a single white‐spotted cow and subsequent genotyping of 172 Brown Swiss cattle revealed two significantly associated completely linked single nucleotide variants (rs722765315 and rs719139527). Both variants are located in the 5′‐regulatory region of the bovine MITF gene, and comparative sequence analysis showed that the variant rs722765315, located 139 kb upstream of the transcription start site of the bovine melanocyte‐specific MITF transcript, is situated in a multi‐species conserved sequence element which is supposed to be regulatory important. Therefore, we hypothesize that rs722765315 represents the most likely causative variant for the white‐spotting phenotype observed in Brown Swiss cattle. Presence of the mutant allele in a heterozygous or homozygous state supports a dominant mode of inheritance with incomplete penetrance and results in a variable extent of coat colour depigmentation.