Substructuring of Scots pine in Europe based on polymorphism at chloroplast microsatellite loci

• Scots pine shows substructuring in its European distribution range.
• Populations from south of the Iberian Peninsula were most divergent at cpSSR loci.
• Populations from Balkans, Central and Northern Europe were genetically homogenous.
• The research shows utility of cpSSR loci for intra- and interspecific gene flow studies in pines.

Scots pine (Pinus sylvestris L.) is a forest forming tree species of great ecological and economic importance in the Northern Hemisphere. Assessment of genetic relationships between populations is needed for a better understanding of demographic and evolutionary processes of the species. We analyzed genetic variation and population structure of 24 native populations of Scots pine across its broad European distribution using a set of 13 polymorphic chloroplast simple-sequence repeats loci (cpSSRs). The number of alleles per locus ranged from 3 to 11 providing a set of 458 different haplotypes (haplotype diversity, He = 0.982). Genetic differentiation in most between-population comparisons was low (FST ranged from 0.00 to 0.08, RST ranged from 0.00 to 0.19) as expected for highly outcrossing and wind pollinated tree species. However, Bayesian clustering analysis revealed at least three distinct genetic clusters corresponding to geographical origin of the analyzed populations. Our results indicate genetic substructuring across the distribution range of Scots pine, and also point to the existence of populations of most likely different history that maintain their genetic identity.