Data from: Evaluation of genetic diversity and population structure of five Chinese indigenous donkey breeds using microsatellite markers

China had the largest population of raising donkeys in the world, however
the number of Chinese indigenous donkey decreased dramatically due to the
increase of agriculture mechanization in the last century. The species has
still been important in China because of its edible and medical value,
therefore the survey on its genetic diversity in China is necessary for
its conservation and utilization. In this study, 15 microsatellite markers
were used to evaluate genetic diversity and population structure of five
Chinese indigenous donkey breeds. The mean values of expected
heterozygosity, allelic richness, and total number of alleles for all the
tested Chinese donkeys were 0.70, 6.04, and 6.28 respectively, suggesting
that the genetic diversity of Chinese indigenous donkeys is rich. The
Bayesian analysis and principal component analysis plot yielded the same
clustering result, which revealed that Guanzhong donkey was the most
differentiated breed in all detected samples, and Jinnan (JN) and
Guangling (GL) were genetically closed together. Additionally, our results
indicated that the heterozygote deficit was severe in two Chinese
indigenous donkey breeds (GL and JN), and it warned us that animal
conservation activities on this species should be considered carefully in
near future.