Table 1.
Genes and markers genotyped for breed analysis.
Fig 1.
Allele frequencies for ASIP, MC1R, and CBD103 by phylogenetic breed relationship.
Breeds are grouped by phylogenetic clade, as described, and sorted within clade by frequency of e and then ay to demonstrate patterns of phenotype expression across interacting genes. Thick black boxes highlight examples of color preference influencing interacting genes: a) Pointer/Setter breeds are commonly seen in solid colors, caused by the KB allele of CBD103 or the e/e genotype of MC1R. Since the solid-color genotypes are epistatic to the dominant alleles of MC1R and all alleles of ASIP, variation at those genes does not follow a trend for color preference. b) Related breeds with high frequency of the ky allele of CBD103 have a more structured pattern of ASIP allele preference. c) Breeds with a preference for the brindle pattern show heterogeneity for KB/kbr (reflective of a kbr phenotype) and high frequency of ay, required for the expression of brindle across the whole body.
Fig 2.
Allele frequencies for MC1R, ASIP, TYRP1, and CBD103 across same-breed populations.
Horizontal black bars indicate within-breed allele distributions that are significantly different (p ≤ 0.00167).
Fig 3.
Identity-by-decent (IBD) haplotype sharing breed relationships connect breeds carrying the T allele for tailless.
Solid black lines represent instances of significant haplotype sharing levels between breeds. The color of the breed names reflects the proposed carrier status of the tailless variant in the sampled members of those breeds, indicating not present (grey), present and permitted within the breed standard (green), and present and not permitted within the breed standard (red). The Dachshund breed shows no significant haplotype sharing with any other breed, however, its highest non-significant haplotype sharing value is with the Swedish Valhund (dashed line). Inset, the Australian Shepherd breed permits natural taillessness.
Fig 4.
Identity-by-decent (IBD) haplotype sharing breed relationships connect breeds carrying the a allele of ASIP.
Solid black lines indicate instances of significant haplotype sharing between breeds. Breed names in purple indicate observed frequency of the a allele within the breed in the present study. Breed names in black indicate that the a allele was not detected within the sampled individuals of that breed. The dashed line connecting the Dalmatian to the Airedale Terrier indicates that no significant haplotype sharing was detected with the Dalmatian, however the highest non-significant level of haplotype sharing was measured with the Airedale Terrier. Inset images show examples of dogs with the recessive black phenotype, A) Shetland Sheepdog, B) Pumi.
Fig 5.
Purebred dogs exhibiting color traits deemed inappropriate by one or more breed registries.
A) Bull Terrier with a brown nose and brown patch above its eye. B) Shetland Sheepdog with piebald white spotting. C) Great Dane with the harlequin pattern on a fawn base color.