Highly informative SSR genotyping reveals large genetic diversity and limited differentiation in European larch (Larix decidua) populations from Romania

European larch (Larix decidua) is naturally distributed at high elevations in Central Europe. Romanian populations of L decidua are scattered in different areas of the country. In this study, we used 12 highly informative genomic simple sequence repeat (SSR) markers for genotyping seven populations from different areas of Romania. The SSR markers were highly variable, with up to 11 alleles per SSR locus and an average polymorphic information content of 0.713. High values of observed (H-o = 0.542) and expected (H-o = 0.738) heterozygosities were observed. Cluster analysis of populations did not group them according to geographical distance, but some clusters contained populations from a similar altitudinal range. The partition of genetic variation revealed that two-thirds of the genetic variation was found within individuals (due to high H-o levels), while only one-sixth of the total genetic variation corresponded to variation among populations. A population structure analysis identified four genetic clusters, and in most cases individuals from a single population were assigned to several genetic clusters. Multivariate principal coordinates analysis confirmed the population structure analysis. SSR markers are a powerful tool for evaluating diversity, relationships, and the genetic structure of Romanian L decidua populations, which have high levels of diversity and low genetic structuration.