Genome-wide exploration of coat color-associated loci in Hokkaido Native Horses, with a novel locus implicated in the roan phenotype.

Genes and loci regulating horse coat color have been investigated in many breeds, but their associations with the 16 coat colors of the Hokkaido Native Horse (HKD) remain unknown. HKDs were classified according to coat-color groups based on pedigree-recorded coat color, and genome-wide association (GWA) analyses were performed. Except for gray and roan, a clear single signal corresponding to the known locus was obtained for each coat color, suggesting that the reported loci are the primary causes of these coat colors. Because gray and roan are difficult to distinguish visually and may therefore have been misclassified, these two phenotypes were re-examined by PCR analysis of the gray-associated locus, and the GWA analyses were repeated. A single significant signal corresponding to the known gray-associated locus was detected for gray in the re-analysis. For roan, two signals were again detected: a signal near the known locus on chromosome 3 and a novel signal on chromosome 8, although only the latter reached statistical significance, suggesting a more complex genetic basis. Among genes with known functions, PIK3C3, which is involved in autophagy, a process associated with melanosome degradation and pigment lightening, was the closest to the chromosome 8 signal. At the chromosome 3 lead SNP, all horses with the GG genotype were roan, but roan and non-roan horses were mixed in the other genotype classes at this SNP and in the genotype classes at the chromosome 8 lead SNP, indicating that genotype-based identification of roan horses is possible only for a subset of animals.