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

Jocelyn Tanaka; Tosso Leeb; James Rushton; Thomas R Famula; Maura Mack; Vidhya Jagannathan; Christine Flury; Iris Bachmann; John Eberth; Sue M McDonnell; Maria Cecilia T Penedo; Rebecca R Bellone

doi:10.3390/genes10100826

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

Genes (Basel). 2019 Oct 19;10(10):826. doi: 10.3390/genes10100826.

Authors

Affiliations

¹ Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA. jltanaka@ucdavis.edu.
² Institute of Genetics, University of Bern, 3001 Bern, Switzerland. tosso.leeb@vetsuisse.unibe.ch.
³ Rowe Equine Ltd, Wotton Under Edge, GLOS GL12 7PP, UK. jamesrushton@rowevetgroup.com.
⁴ Department of Animal Science, University of California, One Shields Ave, Davis, CA 95616, USA. trfamula@ucdavis.edu.
⁵ Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA. Maura.Mack@colostate.edu.
⁶ Institute of Genetics, University of Bern, 3001 Bern, Switzerland. vidhya.jagannathan@vetsuisse.unibe.ch.
⁷ School of Agricultural Forest and Food Sciences, Bern University of Applied Sciences, 3052 Zollikofen, Switzerland. christine.flury@bfh.ch.
⁸ Agroscope, Swiss National Stud Farm, 1580 Avenches, Switzerland. iris.bachmann@agroscope.admin.ch.
⁹ College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA. john.eberth@uky.edu.
¹⁰ Havemeyer Equine Behavior Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center Department of Clinical Studies, Kennett Square, PA 19348, USA. suemcd@vet.upenn.edu.
¹¹ Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA. mctorrespenedo@ucdavis.edu.
¹² Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA. rbellone@ucdavis.edu.
¹³ Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA. rbellone@ucdavis.edu.

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 (P_corrected = 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 (f_mu = 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.

Keywords: Equus caballus; MFSD12; coat color; dilution; pigmentation.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animal Fur / metabolism
Animals
Frameshift Mutation*
Horses / genetics*
Membrane Transport Proteins / genetics
Pigmentation / genetics*

Substances

Membrane Transport Proteins