The Italian donkey (Equus asinus): molecular variability of endangered autochthonous breeds assessed by mitochondrial and microsatellite markers.

In the last century, technology improvement and industrialization have dramatically changed the impact of human activities on natural and agricultural environments, strongly affecting wildlife and the management and use of livestock species. In modern agriculture a few cosmopolitan highly productive breeds are farmed worldwide, while the use of animals for transportation purposes has almost disappeared. As a consequence, diversity contributed by autochthonous livestock species and breeds is being quickly erased. Since domestication (~5000 y.b.p.) donkeys have been widely used by humans in agricultural activities and for transportation of people and goods. In the last century, Italian autochthonous donkeys suffered from a severe reduction in population size that led to the extinction of Cariovilli, Grigio Viterbese and Sant’Alberto donkey breeds. Eight autochthonous Italian breeds are still reared. These are all classified by FAO as critically endangered (Asinara, Pantesco, Grigio Siciliano and Romagnolo) or endangered (Amiatino, Sardo Grigio, Martina Franca and Ragusano) breeds. To evaluate the extant genetic variability of Italian donkey populations, two fragments of the mitochondrial DNA (mtDNA) control region (HVRI, 288 bp) and cytochrome b (274 bp) genes were sequenced and 16 microsatellite loci were typed in 292 individuals from these eight breeds. MtDNA data were then compared with databank sequences of donkeys from Europe, Africa and Asia, two wild subspecies Equus asinus africanus and E.a. somaliensis from Africa and other extant and extinct species of the genus Equus. In Italy 30 different mtDNA control region haplotypes were identified, some of which were never described before. Nucleotide diversity was relatively low, but not far from values detected in other European breeds. Phylogenetic and network analyses disclosed a complex pattern of mtDNA variability and highlighted the presence also in Italy of the two divergent maternal lineages, Somalian and Nubian, which derive from two separated domestication events occurred in Africa from wild ancestors of different subspecies (E. a. somaliensis and E. a. africanus). Sequences were also grouped by geographic areas to shed light on possible underlying patterns due to past migration events. Analysis of microsatellite data revealed the presence of gene flow between breeds and inbreeding.