Evidence for allelic heterogeneity in the KIT gene of roan horses

The genetic background of roan coat color has been investigated by multiple authors in the breeds Belgian draught horse, Shetlandpony, Gotlandpony, Noriker, Murgese, Slovenian Coldblood, Quarter Horse and Icelandic Horse. However, the causal mutation for this color variant could not be detected yet. In this study we genotyped five associated variants in the KIT gene for a sample of 37 roan and 23 non-roan horses from the breeds Noriker, Murgese, Quarter Horse, Welsh Pony, Posavina, Shetlandpony and Icelandic horse, in order to verify and compare them to a newly published KIT variant for the Icelandic horse. The results propose, that the association of the SNP in Intron 17 (ECA3:g.79,543,439A > G) with roan coat color is complete in the Noriker breed and breeds that are genealogically related to it (Slovenian Coldblood, Murgese, Belgian draught horse, Posavina horse). For the Icelandic horse sample, it was shown, that the KIT variant in intron 1 was not linked to the remaining four loci in intron 17, exon 19 and intron 20 of KIT. In the sample of Shetlandponies no variation among genotypes and no association was observed between roan and non-roan horses. The for the Icelandic horse newly associated KIT variant in intron 1 supports the hypothesis of allelic heterogeneity of the roan locus reported by previous studies. The complete sequencing of the KIT region and population specific association analyses in horse breeds of Nordic origin with replication analyses in Warmblooded horse breeds should be able to solve this question of allelic heterogeneity.