Genetic diversity and population structure studies of local olive germplasm are important to safeguard biodiversity, for genetic resources management and to improve the knowledge on the distribution and evolution patterns of this species. In the present study Algerian olive germplasm was characterized using 16 nuclear (nuSSR) and six chloroplast (cpSSR) microsatellites. Algerian varieties, collected from the National Olive Germplasm Repository (ITAFV), 10 of which had never been genotyped before, were analyzed. Our results highlighted the presence of an exclusive genetic core represented by 13 cultivars located in a mountainous area in the North-East of Algeria, named Little Kabylie. Comparison with published datasets, representative of the Mediterranean genetic background, revealed that the most Algerian varieties showed affinity with Central and Eastern Mediterranean cultivars. Interestingly, cpSSR phylogenetic analysis supported results from nuSSRs, highlighting similarities between Algerian germplasm and wild olives from Greece, Italy, Spain and Morocco. This study sheds light on the genetic relationship of Algerian and Mediterranean olive germplasm suggesting possible events of secondary domestication and/or crossing and hybridization across the Mediterranean area. Our findings revealed a distinctive genetic background for cultivars from Little Kabylie and support the increasing awareness that North Africa represents a hotspot of diversity for crop varieties and crop wild relative species.
