Analysis of the Skyros pony breed: population structure and genetic variability

Due to its geographic location, Greece is a crossroad between three continents and its mountainous landscape and numerous islands have lead to the creation of many small populations of distinct and isolated breeds. On the basis of phenotypes and genotypes, seven native breeds were identified. The Skyros pony has a distinct phenotype from those of other breeds. This phenotypic difference seems to be linked to the fact that the Skyros pony is less genetically similar to the other Greek breed than the other breeds are to each other as shown in previous studies. Furthermore, the Skyros pony breed risk status is described as endangered according to the criteria of the Food and Agricultural Organization (DAD-IS). The main reason is that the population is concentrated only in three herds of reduced size.
This study analyses the population structure and describes the genetic variability of the breed using 15 microsatellite markers and available genealogical information. The molecular characterization and the pedigree were also used to investigate the presence of bottleneck. Factorial correspondence analysis and analysis of molecular variance showed that the three herds seemed to be genetically distinct even if the genetic variance between herds was low (5.75%). For the whole population, the mean total number of allele per locus was 5.93. The average Polymorphism Information Content value was relatively high (~ 0.60) as the observed heterozygosity (0.64) and the expected heterozygosity (0.62). The comparison with other studies showed that these values were well within the range for domestic horses but were at the lower end of that range, i.e. with the values from breeds with small population size or recent bottlenecks. However, these values indicated a still substantial genetic diversity in the Skyros breed that could be useful for planning future breeding strategies for the breed conservation. This is consistent with the results of various bottleneck tests, which detected no evidence of bottleneck when considering the whole population but suggested that there was bottleneck in two of the three main herds of Skyros pony. Comparisons between DNA-based and pedigree-based results showed that the loss of genetic diversity has probably occurred before the beginning of breed registration.