Genetic characterization of the Miyako horse based on polymorphisms of microsatellites and mitochondrial DNA

Abstract

To help plan conservation of the endangered Miyako horse, a biological resource of the Miyako Islands in Japan, we characterized the genetics of the breed by genotyping 32 microsatellites and identifying mitochondrial DNA haplotypes. We also calculated genetic distances between individuals based on the proportion of shared alleles and visualized the genetic relationships with a phylogenetic tree. Two important results were obtained. One is that accurate pedigree registration of the horse by using microsatellites is possible, as the exclusion power of parentage testing is 0.999998. Another is that the current genetic diversity of the horses was clarified. The average number of alleles, observed heterozygosity and expected heterozygosity were 4.2, 0.701 and 0.649, respectively, for the 35 analyzed horses. The probability values for bottleneck models (infinite allele model: 0.00000; stepwise mutation model: 0.00026; and two-phase model: 0.00000) suggested that Miyako horses have experienced a recent genetic bottleneck. Only one mitochondrial haplotype was identified. Consequently, genetic diversity within the population is relatively well-maintained despite a very small population size (41 at the time of the study), and the first priority in conservation of the Miyako horse is to increase the population size.

Genetic diversity and population structure of three traditional horse breeds of Bhutan based on 29 DNA microsatellite markers

“…In general, the adjusted genetic diversity of Bhutanese traditional horses for the common loci was high and comparable to American horses’ study involving 50 breeds [ 27 ] (mean number of alleles MNA 7.5; H O 0.74, H E 0.75, F IS 0.02) ( S3 Table ) and five Indian native horses (MNA 14; N E 6.62; H O 0.72) [ 28 ] for 24 common loci ( S4 Table ). By breed, the genetic diversity of Bhutanese traditional horses was similar to the native Korean Halla horse [ 29 ] ( S7 Table ) but higher than endangered Japanese breeds ( S5 and S6 Tables) as expected; Yonaguni horse ( N A 4.3; H O 0.59; H E 0.6) [ 30 ], Kiso horse ( N A 6.3, H O 0.66, H E 0.65) [ 31 ] and Miyako ( N A 4.2; H O 0.70; H E 0.649) [ 32 ].…”

Genetic diversity and relationships among native Japanese horse breeds, the Japanese Thoroughbred and horses outside of Japan using genome‐wide SNP data

“…There are currently very few breeding Miyako horses, and the breed is in danger of extinction (Senju et al . ). If deemed necessary, given the genetic similarities, breed managers could consider managing the Miyako and Yonaguni populations collectively.…”

Decreased genetic diversity in Kiso horses revealed through annual microsatellite genotyping

“…However, we believe it is essential to perform continuous microsatellites genotyping so that we can provide timely evaluations of genetic diversity. In addition, our microsatellite-based genetic survey of this endangered breed should be a valuable reference for conservation of other endemic Japanese horses with a small population size [6,[9][10][11].…”