Genetic and chemical variation analysis of species of Polygonatum: Implications for diversity assessment and elite germplasm screening

Polygonati Rhizoma, derived from three medicinal Polygonatum species ( P. cyrtonema , P. sibiricum , and P. kingianum ), is a renowned traditional medicinal and edible resource with a history exceeding two thousand years. Decades of unregulated harvesting have severely depleted its wild resources. However, comprehensive evaluations integrating both genetic backgrounds and phytochemical variations remain limited, hindering effective germplasm conservation. We evaluated 30 naturally distributed Polygonatum accessions, with a specific focus on major geo-authentic distribution regions in central China. Genetic diversity, assessed via ISSR and SSR markers, revealed high polymorphism with an average of 35.61% polymorphic loci (ISSR+SSR) and significant population differentiation (G ST = 0.3392–0.5436). Chemical profiling of eight nutritional and bioactive components demonstrated substantial variation; for instance, polysaccharide contents widely ranged from 5.09% to 24.83%. Integration of these datasets using the Entropy Weight Method and Grey Relational Analysis (EWM-GRA) identified polyphenols and polysaccharides as core quality indicators, serving as the primary determinants with weights of 22.914% and 16.098%, respectively. To eliminate interspecies bias, accessions were ranked independently within their respective species. Specifically, P. cyrtonema accession W-21, P. sibiricum accession W-6, and P. kingianum accession W-7 emerged as the elite germplasms for their respective species. Furthermore, simple linear regression analysis mathematically decoupled genetic diversity from comprehensive quality ( P = 0.571). This indicates that while genetic backgrounds define species boundaries, the superior phytochemical profiles of elite germplasms are predominantly driven by local environmental adaptations rather than baseline genetic diversity alone, providing a scientific foundation for prioritizing geo-authentic origins in future cultivation.