Evaluating SSR marker transferability and plastid barcode variation in native <i>Populus</i> and <i>Salix</i> species of Türkiye

<i>Populus</i> and <i>Salix</i> species are key components of forest and riparian ecosystems and hold substantial economic value in forestry, bioenergy, and restoration practices. In Türkiye, these genera are widely distributed across diverse ecological zones, yet regional molecular data remain limited. In this study, I examined genetic relationships among six native species-<i>Populus nigra</i> L<i>., Populus alba</i> L<i>., Populus tremula</i> L<i>., Populus euphratica</i> Olivier, <i>Salix alba</i> L., and <i>Salix caprea</i> L.<i>-</i>using an integrative molecular approach. Twelve nuclear microsatellite (simple sequence repeats; SSR) markers and three plastid DNA barcode regions (<i>matK, rbcL, trnH-psbA)</i> were employed to assess marker performance, genetic variation, and species-level relationships. The analyses revealed clear genetic differentiation between <i>Populus</i> and <i>Salix</i> and substantial variation among <i>Populus species</i>. SSR loci detected both conserved and lineage-specific alleles, with limited allele sharing between genera, while plastid barcodes showed marker-specific patterns of sequence variation and phylogenetic resolution. Among the plastid regions, <i>matK</i> provided the strongest discriminatory signal, whereas <i>rbcL</i> was more conservative and <i>trnH-psbA</i> exhibited higher variability. <i>P. tremula and P. nigra</i> displayed higher levels of sequence and allelic variation compared with the other taxa, whereas <i>P. euphratica</i> showed a more distinct genetic profile. The combined use of nuclear SSRs and plastid barcodes provided complementary insights into genetic structure and evolutionary relationships among selected <i>Populus</i> and <i>Salix</i> species. Although limited in taxon and marker coverage, this study contributes regionally focused molecular data from a biogeographically underrepresented area and provides a foundation for future multilocus and genome-wide investigations of Salicaceae diversity in Türkiye.