Genetic diversity and phylogeographic structure of sixteen Mediterranean chicken breeds assessed with microsatellites and mitochondrial DNA

• Twenty seven microsatellite were genotyped in 16 Mediterranean chicken breeds.
• The D-loop region were sequenced in 160 samples.
• Six chicken breeds show significant inbreeding level.
• The genetic variability is comparable to other European breeds.
• Mediterranean breeds are mainly related to haplogroup E.

The genetic diversities and relationships among 16 local breeds of chicken originating from five countries (Italy, Spain, Serbia, Albania and Republic of Malta) within the Mediterranean basin were assessed by sequencing part of the mitochondrial DNA (mtDNA) D-loop region and by genotyping individuals at 27 autosomal microsatellite loci. The aim was to study the microevolution of chicken on the northern shores of the Mediterranean and to determine their present genetic status. A 506 bp fragment of the mtDNA control region was sequenced in 160 individual DNA samples. The mtDNA sequence polymorphisms nomenclature that is normally used in these studies suggests that the Mediterranean chicken breeds under investigation are related to haplogroup E. A total of 465 blood samples were collected and utilised for microsatellite analysis. Six breeds (Ancona, Livornese Bianca—Italy; Pita Pinta Asturiana, Gallina de Sobrarbe—Spain; Albanian population—Albania; and the Maltese Black—Malta) showed significant high levels of inbreeding. About 22% of the total genetic variation observed was due to variability between populations. STRUCTURE analysis confirmed the breed variability result (FST=0.22) also observed in the Neighbor-Net dendrogram.These results strongly allude that the 16 Mediterranean chicken breeds studied originated from three distinct maternal lineages and retain moderate levels of autosomal genetic diversity.