Comprehensive genetic testing combined with citizen science reveals a recently characterized ancient MC1R mutation associated with partial recessive red phenotypes in dog

Abstract

Background: The Melanocortin 1 Receptor (MC1R) plays a central role in regulation of coat color determination in various species and is commonly referred to as the "E (extension) Locus". Allelic variation of the MC1R gene is associated with coat color phenotypes E^M (melanistic mask), E^G (grizzle/domino) and e^1-3 (recessive red) in dogs. In addition, a previous study of archeological dog specimens over 10,000 years of age identified a variant p.R301C in the MC1R gene that may have influenced coat color of early dogs.

Results: Commercial genotyping of 11,750 dog samples showed the R301C variant of the MC1R gene was present in 35 breeds or breed varieties, at an allele frequency of 1.5% in the tested population. We detected no linkage disequilibrium between R301C and other tested alleles of the E locus. Based on current convention we propose that R301C should be considered a novel allele of the E locus, which we have termed e^A for "e ancient red". Phenotype analysis of owner-provided dog pictures reveals that the e^A allele has an impact on coat color and is recessive to wild type E and dominant to the e alleles. In dominant black (K^B/*) dogs it can prevent the phenotypic expression of the K locus, and the expressed coat color is solely determined by the A locus. In the absence of dominant black, e^A/e^A and e^A/e genotypes result in the coat color patterns referred to in their respective breed communities as domino in Alaskan Malamute and other Spitz breeds, grizzle in Chihuahua, and pied in Beagle.

Conclusions: This study demonstrates a large genotype screening effort to identify the frequency and distribution of the MC1R R301C variant, one of the earliest mutations captured by canine domestication, and citizen science empowered characterization of its impact on coat color.

Keywords: Ancient; Canine; Coat color; Dog; Domino; Eumelanin; Grizzle; MC1R; Pheomelanin; Reduced-function variant.

Fig. 1

Allele frequency of the R301C variant in 35 breeds and breed varieties. The black line indicates the allele frequency of R301C in each breed or breed variety. The number of dogs in each breed analyzed for the presence of the R301C variant is indicated after the breed label

Fig. 2

The e^A allele associated domino pattern is recessive to the wild type E allele. Mating of recessive red (cream colored) e¹/e¹ sire to E/e^A wolf sable dam in the Tamaskan Dog breed, resulting in four normal wolf sable puppies with E/e¹ genotype and four puppies with domino pattern, of which two express domino on wolf sable and two express domino on recessive black. In newborns, domino pattern is visible as large pheomelanin colored areas on both sides of the muzzle, pheomelanin areas around the eyes and overall as a lighter coat color of the body with dark bar of hair remaining on the back side around the vertebra

Fig. 3

Photos representing the phenotypic impact of the e^A allele. The e^A/e^A and e^A/e¹ genotypes mask the presence of K^B (or k^br) at the K locus to produce phenotypes representing the dogs A locus genotype; a^y fawn in Cirneco dell’Etna (a) and in Drever (b); differing from the rare K^B solid eumelanin shade in Cirneco dell’Etna (in which the eumelanin shade is brown due to variants in the TYRP1 gene) (c); or k^br brindle patterning displayed in Plott (d); a saddle tan modified a^t tan point in mixed breed dog (e-f) instead of solid dominant black in Labrador Retriever (g). The e^A phenotype in dogs expressing patterns of the A locus a^y fawn; is cream in Berger d’Auvergne (h-i) and domino in Finnish Lapphund (j) compared to fawn in Berger d’Auvergne (k) and heavily shaded fawn in Finnish Lapphund (l); a^w wolf sable also presents as color pattern domino in Siberian Husky (m) and in a mixed breed dog (n), compared to typical wolf sable in Siberian Husky (o) and in mixed breed dog (p); similarly a^t tan point shows a color pattern called “grizzle” in Chihuahua (q) or reduced saddle tan patterning called “pied” in Beagle (r); (j) compared to normal tan points in Chihuahua (s) or typical saddle tan patterning in Beagle (t); a recessive black dog manifests tan points with pale hair root in Alaskan Klee Kai (u-v) or wolf sable in Tamaskan Dog (w) instead of uniform recessive black in German Shepherd Dog (x). Taken together, ancient red e^A phenotypes manifest as a wide variety of partial recessive red coat colors expressing less eumelanin compared to dogs with wild type E, while no eumelanin is expressed in e recessive red exemplified by a Cirneco dell’Etna (y)