Frameshift Variant in MFSD12 Explains the Mushroom Coat Color Dilution in Shetland Ponies

Abstract

Mushroom is a unique coat color phenotype in Shetland Ponies characterized by the dilution of the chestnut coat color to a sepia tone and is hypothesized to be a recessive trait. A genome wide association study (GWAS), utilizing the Affymetrix 670K array (MNEc670k) and a single locus mixed linear model analysis (EMMAX), identified a locus on ECA7 for further investigation (Pcorrected = 2.08 × 10−10). This locus contained a 3 Mb run of homozygosity in the 12 mushroom ponies tested. Analysis of high throughput Illumina sequencing data from one mushroom Shetland pony compared to 87 genomes from horses of various breeds, uncovered a frameshift variant, p.Asp201fs, in the MFSD12 gene encoding the major facilitator superfamily domain containing 12 protein. This variant was perfectly concordant with phenotype in 96 Shetland Ponies (P = 1.15 × 10−22), was identified in the closely related Miniature Horse for which the mushroom phenotype is suspected to occur (fmu = 0.02), and was absent in 252 individuals from seven additional breeds not reported to have the mushroom phenotype. MFSD12 is highly expressed in melanocytes and variants in this gene in humans, mice, and dogs impact pigmentation. Given the role of MFSD12 in melanogenesis, we propose that p.Asp201fs is causal for the dilution observed in mushroom ponies.

Identification of a Missense Variant in MFSD12 Involved in Dilution of Phaeomelanin Leading to White or Cream Coat Color in Dogs

“…Variants in this gene have recently been associated with skin pigmentation in humans [16,17] and grey coat color in mice [17] resulting from dilution of the phaeomelanin pigment with normal eumelanin production. In addition, variants of this gene have also been associated with the mushroom coat color dilution in ponies [18]. Thus, to identify the causal variant linked to the phaeomelanin dilution in dogs, we imputed 444 variants, identified through the 577 dog sequencing data (DBVDC) [15], spanning 2 Mb (chr20:54.8–56.8 Mb) on the chromosome 20 locus.…”

“…Looking at human pigmentation data, MFSD12 was recently associated with diluted skin pigmentation [16,17] and since we found an exactly homologous variant of MFSD12 (rs751585493) in the human database, in South Asian populations we anticipate that this SNV is also associated with phaeomelanin dilution in humans, enriching the list of variants linked to skin pigmentation in mammals. The MFSD12 gene was, very recently, also associated with the Mushroom coat color in horses [18] and with the grey coat color in mice [17], resulting from dilution of the phaeomelanin pigment with normal eumelanin production. Functional analyses indicate that MFSD12 is involved in lysosomal biology but not in eumelanosomes [16,17], answer the question of why eumelanin is not affected by these variants.…”

Meta-analysis of the genetic loci of pigment pattern evolution in vertebrates

“…Association studies conducted on thousands of samples are now reaching a point where small-effect loci are detectable, under the conditions that these variants are common : for instance, several GWAS studies of skin pigmentation levels have uncovered an amino-acid polymorphism of MFSD12 as a determinant of colour variation across several continents (Adhikari et al, 2019;Crawford et al, 2017;Feng et al, 2021;Lona-Durazo et al, 2019). This gene is now a candidate that is also showing association signals in domestic animal studies (Hédan et al, 2019;Tanaka et al, 2019), suggesting it is effectively a hotspot of pigment variation. While human GWAS studies are systematically curated and will undoubtedly lead to powerful meta-analyses (Buniello et al, 2019), and while infrastructure is being built to integrate these data with laboratory model systems (Shefchek et al, 2020), there is a lack of resources to compile data from evolutionary and bred gene-totrait relationships beyond these organisms.…”

Identification of W13 in the American Miniature Horse and Shetland Pony Populations

“…Variants that impact base coat color have been identified in agouti signaling protein ( ASIP ) and melanocortin 1 receptor ( MC1R ) [ 5 , 6 , 7 ]. Six variants in five genes have been shown to dilute pigment, and these are known as cream (Cr), pearl (Prl), champagne (Ch), dun (D), mushroom (Mu), and silver (Z) [ 8 , 9 , 10 , 11 , 12 , 13 ]. Variants in seven genes ( KIT , EDNRB , TRPM1 , MITF , PAX3 , RFWD3 , STX17 ) have been documented to cause white patterning in domestic horses [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 ].…”