Status of the genetic diversity and population structure of the Pêga donkey

Pedigree analysis was extended to the Pêga donkey population in order to evaluate the status of genetic diversity and population structure. All parameters were computed for three reference populations of animals born between 2004 and 2014: all animals, animals with mouse gray coat color, and animals with roan coat color. Although the average inbreeding coefficient observed was low (about 3 %), highly inbred animals are present in the current population. The effective population size based on the individual inbreeding rate was 35, while the effective population size based on the individual coancestry rate was about three times higher. The number of equivalent subpopulations was at around three, indicating that the Pêga donkey population is highly structured. There is no evidence of differentiation between subpopulations based on the coat color of the animals (Nei's minimum distance 0.10 %). The breeding policy of Pêga donkeys is predominantly intra-herd. The loss of genetic diversity since the founder generations can be considered small in Pêga donkeys (1.25 %). The excessive contribution of few ancestors to the gene pool may lead to narrower bottlenecks in the pedigree of this population in the future. The long generation interval in Pêga donkeys (10.7 years) may be considered an advantage to reduce the increase in inbreeding and to maintain the genetic diversity of these animals.