Development and Application of EST-SSR Markers to Assess Genetic Diversity and Structure of Eleutherococcus senticosus for Conservation and Breeding

Eleutherococcus senticosus, a medicinally important woody plant, is widely used in pharmaceuticals and functional foods due to its bioactive compounds. Its wild populations are facing severe threats due to over-harvesting. To inform scientific conservation and sustainable utilization strategies, this study aimed to comprehensively assess its genetic background. We developed 13 highly polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from full-length transcriptome data, with an average polymorphism information content (PIC) of 0.52. Using these markers, we systematically evaluated the genetic diversity of 405 individuals from 22 natural populations across Northeast China. The results indicate that E. senticosus maintains moderate genetic diversity at the species level (mean expected heterozygosity He = 0.43), but substantial variation exists among populations. The Linjiang population showed the highest diversity (He = 0.58), whereas peripheral populations such as Tonghua (He = 0.31) and Huinan (He = 0.32) exhibited lower diversity. Analysis of molecular variance (AMOVA) revealed that genetic variation primarily resided within populations (66.3%), but moderate differentiation among populations was also detected (Fst = 0.21). Both structure analysis and clustering consistently divided all populations into two major genetic lineages. Frequent gene flow (e.g., Nm > 10 between Raohe and Hulin) and high genetic homogeneity were observed among populations in the core distribution area (e.g., Raohe, Jixi, Hulin), whereas several peripheral populations displayed significant genetic distinctiveness and isolation. This study provides the first macro-scale insight into the population genetic structure of E. senticosus, offering crucial molecular tools and a scientific basis for in situ and ex situ conservation, core collection establishment, and future genetic improvement of this species.