Evaluating genetic diversity and structure of a wild hop ( Humulus lupulus L.) germplasm using morphological and molecular characteristics

Humulus lupulus L., is an economically and ecologically important plant species, which has suffered habitat degradation throughout the Hyrcanian forests (Northern Iran). Towards conservation and exotic breeding germplasm assessment, we conducted a survey in the Hyrcanian forests: 15 wild populations (WPs) were located and 54 samples collected. Genetic diversity and population structure were assessed by scoring sequence-related amplified polymorphism markers (SSR, ISSR, and RAPD) and morphological features. Molecular marker analysis showed that RAPDs (232) and ISSRs (77) produced more polymorphic bands compared to SSRs (64) per marker. SSRs exhibited a higher PIC average value (0.64), than RAPDs (0.24) and ISSRs (0.54). Cluster analyses based on the SSR markers to a high degree discriminated WPs based on geographical regions and were more congruent with morphologic traits than the ISSR–RAPD-based clustering. The ΔK parameter of structure analysis showed five clusters. The grouping of the WPs based on the structure analysis was congruent with the SSR clustering to some extent. The results confirmed that SSR markers are effective tools to detect the genetic diversity in hops, but employing higher number of molecular markers (more SSRs), which have a higher polymorphism and prevalence in the genome, or application of NGS SNPs in the identification and genetic relationship of hop indigenous populations, is recommended.