A KIT Variant Associated with Increased White Spotting Epistatic to MC1R Genotype in Horses (Equus caballus)

SIMPLE SUMMARY: Although over 40 genetic variants are known to influence white spotting and markings on the horse, many still have unknown genetic causes. Furthermore, some seem to be influenced by pigmentation (base coat color) genes. We investigated two horses demonstrating a heritable white spotting pattern of no known genetic cause. Through sequencing of the coding region of candidate genes, we identified a mutation in the KIT proto-oncogene, receptor tyrosine kinase (KIT) gene changing the coded amino acid, predicted to be deleterious to protein function. We further evaluated this variant in a population of 147 horses, characterized using photographs scored by three independent observers using a standardized Average Grade of White score. The KIT mutation is significantly associated with a quantitative increase in white pattern (p = 3.3 × 10(−12)) and demonstrates an influence of the MC1R Extension locus. We also report a complete link between the previously reported KIT W19 allele and this mutation. We propose to name this mutation W34, following established nomenclature. Given the quantitative effect on white markings and MC1R influence, genetic testing for this allele can be of value for horse owners that desire to select for white patterns. ABSTRACT: Over 40 identified genetic variants contribute to white spotting in the horse. White markings and spotting are under selection for their impact on the economic value of an equine, yet many phenotypes have an unknown genetic basis. Previous studies also demonstrate an interaction between MC1R and ASIP pigmentation loci and white spotting associated with KIT and MITF. We investigated two stallions presenting with a white spotting phenotype of unknown cause. Exon sequencing of the KIT and MITF candidate genes identified a missense variant in KIT (rs1140732842, NC_009146.3:g.79566881T>C, p.T391A) predicted by SIFT and PROVEAN as not tolerated/deleterious. Three independent observers generated an Average Grade of White (AGW) phenotype score for 147 individuals based on photographs. The KIT variant demonstrates a significant QTL association to AGW (p = 3.3 × 10(−12)). Association with the MC1R Extension locus demonstrated that, although not in LD, MC1R e/e (chestnut) individuals had higher AGW scores than MC1R E/- individuals (p = 3.09 × 10(−17)). We also report complete linkage of the previously reported KIT W19 allele to this missense variant. We propose to term this variant W34, following the standardized nomenclature for white spotting variants within the equine KIT gene, and report its epistatic interaction with MC1R.