Development of a method for simultaneously genotyping multiple horse coat colour loci and genetic investigation of basic colour variation in Thoroughbred and Misaki horses in Japan

In order to develop a genotyping method that can be used in the registration procedure for Thoroughbreds, we developed a method for simultaneously genotyping multiple coat colour genes on the basis of single nucleotide polymorphism typing by using the SNaPshot^TM technique. This method enabled precise and reasonable detection of causal mutations; it was effective for genotyping of MC1R, ASIP, and SLC45A2 at the Extension (E), Agouti (A), Cream dilution (C) loci, and the possibility of identification of rare variants of MC1R, EDNRB and KIT at the E, Overo (O) and Sabino 1 (SB1) loci, respectively, was also indicated. It was considered that this genotyping method would provide information not only for the registration of Thoroughbreds but also for the preservation of phenotypic characters, such as coat colour, of endangered Misaki native horses in Japan. Therefore, genetic variations at the five coat colour loci were investigated in 1111 Thoroughbred and 99 Misaki native horses. Allele frequencies at the polymorphic E and A loci were estimated, and the proportions of basic coat colours that could be expected in the Thoroughbred population were bay, 0.662; black, 0.070; chestnut, 0.268. In the Misaki population, they were bay, 0.792; black, 0.129; chestnut, 0.080. The data presented were the first of its kind on genetic coat colour variation, and will be important with regard to the registration of Thoroughbreds and the management of Misaki horses.