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Coat color in Holstein dairy cattle is primarily controlled by the  melanocortin 1 receptor  ( MC1R ) gene, a central determinant of black (eumelanin) vs. red/brown pheomelanin synthesis across animal species. The major  MC1R  alleles in Holsteins are Dominant  Black  ( MC1R D  ) and  Recessive Red  ( MC1R e  ). A novel form of dominant red coat color was first observed in an animal born in 1980. The mutation underlying this phenotype was named  Dominant Red  and is epistatic to the constitutively activated  MC1R D  . Here we show that a missense mutation in the  coatomer protein complex ,  subunit alpha  ( COPA ), a gene with previously no known role in pigmentation synthesis, is completely associated with Dominant Red in Holstein dairy cattle. The mutation results in an arginine to cysteine substitution at an amino acid residue completely conserved across eukaryotes. Despite this high level of conservation we show that both heterozygotes and homozygotes are healthy and viable. Analysis of hair pigment composition shows that the Dominant Red phenotype is similar to the  MC1R  Recessive Red phenotype, although less effective at reducing eumelanin synthesis. RNA-seq data similarly show that Dominant Red animals achieve predominantly pheomelanin synthesis by downregulating genes normally required for eumelanin synthesis. COPA is a component of the coat protein I seven subunit complex that is involved with retrograde and cis-Golgi intracellular coated vesicle transport of both protein and RNA cargo. This suggests that Dominant Red may be caused by aberrant MC1R protein or mRNA trafficking within the highly compartmentalized melanocyte, mimicking the effect of the Recessive Red loss of function  MC1R  allele.

Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene