Population Analysis Identifies 15 Multi-Variant Dominant White Haplotypes in Horses

Abstract

The influence of a horse’s appearance on health, sentimental and monetary value has driven the desire to understand the etiology of coat color. White markings on the coat define inclusion for multiple horse breeds, but they may disqualify a horse from registration in other breeds. In domesticated horses (Equus caballus), 35 KIT alleles are associated with or cause depigmentation and white spotting. It is a common misconception among the general public that a horse can possess only two KIT variants. To correct this misconception, we used BEAGLE 5.4-phased NGS data to identify 15 haplotypes possessing two or more KIT variants previously associated with depigmentation phenotypes. We sourced photos for 161 horses comprising 12 compound genotypes with three or more KIT variants and employed a standardized method to grade depigmentation, yielding average white scores for each unique compound genotype. We found that 7 of the 12 multi-variant haplotypes resulted in significantly more depigmentation relative to the single-variant haplotypes (ANOVA). It is clear horses can possess more than two KIT variants, and future work aims to document phenotypic variations for each compound genotype.

Coloration in Equine: Overview of Candidate Genes Associated with Coat Color Phenotypes

“…The proto-oncogene c-kit is located on chromosome 3 in horses and affects the survival, migration, and differentiation of melanocytes. It is a major candidate gene for the formation of white coat color [ 78 , 79 , 80 ]. Previous studies have shown that four white coat color traits, Dominant White, Tobiano, Sabino, and Roan, are associated with the KIT gene, as depicted in Table 3 .…”

“…This finding may help explain the appearance of the cryptic Tobiano phenotype [ 36 , 86 ]. Similarly, Brooks et al [ 80 ] identified a single nucleotide polymorphism resulting from a T and A base substitution in intron 16 and a subsequent deletion in exon 17, leading to the formation of Sabino 1 (SB1). However, this specific polymorphism cannot fully account for the various Sabino types observed.…”