Genetic characterization of phenotypic traits in endangered Taishu horse breed and their breeding strategy

•The variants in MC1R and ASIP gene showed polymorphisms in Taishu horse population.•g.66608679T/C in MSTN gene showed polymorphisms in Taishu horse population.•Black Taishu horses had unique trait of changing to light brown color in summer.•Rare coat color is conserved via breeding strategy based on MC1R and ASIP genotypes. The Taishu horse is a native Japanese breed threatened with extinction. It is important to genotype the causative genes of rare phenotypes in endangered breeds because unique genetic traits might be lost unless a breeding strategy for conservation is constructed. In the present study, nine single-nucleotide variants and three indels of nine genes related to coat color, body composition, and gait were genotyped in 56 Taishu horses. Of these, only three genes were polymorphic. The observed coat color phenotypes coincided with the estimated phenotype from the genotypes, whereas black horses showed specific phenotypes that were generally black in winter but turned light brown in summer. No DNA polymorphisms in ligand-dependent nuclear receptor corepressor-like gene and very few polymorphisms in myostatin gene were identified. While means of withers height, chest circumference, cannon circumference, and body length were 122.8, 143.1, 16.9, and 130.2 cm, respectively, no relationship was found between the variants investigated and the body composition measurements. The gaited allele of doublesex and mab-3 related transcription factor 3 gene was not observed and the estimated phenotypes coincided with the observed phenotype, trot. Genotypes of coat color in the Taishu horses are essential for the construction of breeding strategies to conserve black and chestnut horses, which are much less common than bay horses. These results may help breeders construct breeding strategies to conserve rare phenotypic traits in this breed. This initiative will also be beneficial for breeding programs of other native Japanese horses, such as Noma and Miyako, whose numbers are declining.