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This study was undertaken to reveal the relationship between genetic variations and the basic coat color classification system in Jeju horses. Genetic variations of the melanocortinreceptor 1(MC1R) and agouti signaling protein(ASIP) genes were investigated using pyrosequencing technique. A nucleotide substitution mutation for MC1R g.901C>T and an ASIP 11-bp deletion mutation were screened. Black horses had MC1R E^+/- (E^+/E^+ or E^+/E^e) and ASIP A^a/A^a genotypes. In contrast, chestnut horse genotypes were MC1R E^e/E^e and ASIP -/-. Thus, black and bay horses have at least one dominant MC1R allele, E^+, whereas chestnut horses have homozygous recessive alleles E^e/E^e. This suggests that the MC1R genotypes determine chestnut or black/bay coat color, regardless of the genotype distribution of ASIP. In addition, the horses with MC1R E^+/- and a dominant ASIP A^A/- allele showed bay coat color, but not black, suggesting that the ASIP A^A allele represses black coat color development in the hairs of the body, but not in the mane and all four legs. Pedigree analysis showed a consistent relationship between the genotype distribution of the MC1R and ASIP genes and basic coat color patterns, even in the F_1 progeny. The results of this study revealed the relationship between the coat color phenotype and genetic background and suggested that useful information may be provided for molecular breeding of Jeju horses.

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