Genetic diversity analysis and parentage verification of Taishu horses using 31 microsatellites

The Taishu horse in Tsushima is one of eight Japanese native breeds. The breed is on the verge of extinction due to a rapid decrease in numbers since the 1960s owing to motorization in Japan. In this study, we aimed to confirm the pedigree information of 52 horses by genotyping 31 microsatellites in order to avoid inbreeding. Parentage verification failed to identify genetic contradictions among trios (sires, dams, and foals) registered with the Japan Equine Affairs Association (JEAA). Pedigree information registered at the JEAA was obtained and adequately understood. Additionally, the genetic diversity of the Taishu horses was evaluated and compared with those of other Japanese native breeds. The average values for the number of alleles, observed heterozygosity, expected heterozygosity, and inbreeding coefficient were 4.7, 0.643, 0.632, and −0.02, respectively. Using the Structure software, the 52 horses were classified into three subgroups based on the individuals with more than 50% of specific genetic components. The phylogenetic trees created based on neighbor-joining classification tended to be consistent among the stallions. The effective population size was 27.5 and lower than that required for maintaining 90% genetic variation in the source population over a period of 100 years (47.5). Compared with the other Japanese breeds, the Taishu horse population included in the current study exhibited moderate genetic diversity. Our study will contribute to reconsideration of the breeding strategy of Taishu horses.