Pigment Intensity in Dogs is Associated with a Copy Number Variant Upstream of KITLG

Abstract

Dogs exhibit a wide variety of coat color types, and many genes have been identified that control pigment production, appearance, and distribution. Some breeds, such as the Nova Scotia Duck Tolling Retriever (NSDTR), exhibit variation in pheomelanin pigment intensity that is not explained by known genetic variants. A genome-wide association study comparing light red to dark red in the NSDTR identified a significantly associated region on canine chromosome 15 (CFA 15:23 Mb–38 Mb). Coverage analysis of whole genome sequence data from eight dogs identified a 6 kb copy number variant (CNV) 152 kb upstream of KITLG. Genotyping with digital droplet PCR (ddPCR) confirmed a significant association between an increased copy number with the dark-red coat color in NSDTR (p = 6.1 × 10−7). The copy number of the CNV was also significantly associated with coat color variation in both eumelanin and pheomelanin-based Poodles (p = 1.5 × 10−8, 4.0 × 10−9) and across other breeds. Moreover, the copy number correlated with pigment intensity along the hair shaft in both pheomelanin and eumelanin coats. KITLG plays an important role in melanogenesis, and variants upstream of KITLG have been associated with coat color variation in mice as well as hair color in humans consistent with its role in the domestic dog.

A Third MLPH Variant Causing Coat Color Dilution in Dogs

“…In mudis, this color is referred to as “grey-brown”. The mudis in (E) and (F) have two copies of the recessive e allele of the MC1R gene, that affects phaeomelanin and results in varying shades of cream [ 4 , 10 , 13 , 14 , 15 , 16 ]. Additionally, the mudi in (E) is homozygous for d 3 , thus showing grey pigmentation on the nose and eye rims, and a lightened eye color.…”

“…The effects of MLPH variants on melanosome transport and pigmentation are distinct from the recently identified variants of phaeomelanin-based pigment intensity, which also perturb the perceived depth of coloration, although resulting coat colors are varying shades of red, cream, and white [ 4 ]. Nevertheless, the previously identified d 1 and d 2 MLPH variants do not explain all of the dilute coat color phenotypes in canids, and a recent report suggests that additional coat color alleles are likely present at low frequency throughout the canine population [ 2 , 3 , 5 ].…”

An Agouti-Signaling-Protein Mutation is Strongly Associated with Melanism in European Roe Deer (Capreolus capreolus)

“…Altogether and regardless of other genetic reasons for melanism, e.g., [17][18][19][20][21][22][23], investigation of segregation of both alleles, mutated and non-mutated, in a set of 495 samples produced a perfect association resulting in extremely high statistical support under different scenarios and providing strong arguments that the mutation c.33.G>T causes the black phenotype in European roe deer. Considering the high frequency of melanistic individuals in the North-West German lowland population, it cannot be excluded that melanism had a selective advantage (e.g., camouflage) as previously discussed for other species [3,18,24].…”

Five genetic variants explain over 70% of hair coat pheomelanin intensity variation in purebred and mixed breed domestic dogs

“…However, dogs that were homozygous for the mutation still showed variation in pheomelanin dilution within some breeds, suggesting that pheomelanin dilution is a multigenic trait both across and within breeds. Similarly, a third study identified a copy number variant upstream of the KIT ligand gene ( KITLG ) that was predictive of red intensity in Nova Scotia Duck Tolling Retriever and Poodle [ 32 ], but not in two of the most common (in the United States [ 33 ]) and phenotypically variable breeds: Golden Retriever and Labrador Retriever. In this study, our aim was to increase understanding of the genetic underpinnings of coat pheomelanin intensity variation in dogs by testing whether there are additional loci that affect intensity across dog breeds, and investigating how these loci might interact.…”