Genetic diversity and core collection of Polygonati Rhizoma in China via SSR markers

Polygonati Rhizoma is a widely cultivated herb in China, renowned for its culinary and medicinal uses. Despite extensive research, comprehensive studies on the population genetic diversity and core collection construction of medicinal Polygonatum species remain scarce. To address this, we conducted a thorough population genetic analysis and constructed a core collection for 175 accessions from three pharmacopoeial species and one closely related species using 18 highly polymorphic SSR primers. Our results reveal significant variation in genetic diversity among the four studied species of Polygonati Rhizoma, ranked from highest to lowest genetic diversity as follows: Polygonatum cyrtonema Hua ( P. cyrtonema ), Polygonatum sibiricum Red. ( P. sibiricum ), Polygonatum kingianum Coll. et Hemsl. ( P. kingianum ), and Polygonatum zanlanscianense Pamp. ( P. zanlanscianense ). Analysis of molecular variance (AMOVA) indicates that the majority of genetic variation occurs within populations, and a positive correlation exists between genetic distance and geographic distance. Cluster and population structure analyses identified three primary subgroups: Group 1, comprising P. kingianum ; Group 2, including the majority of P. sibiricum and P. zanlanscianense ; and Group 3, primarily consisting of P. cyrtonema and P. sibiricum from Sichuan Province. A core collection was constructed through stepwise clustering based on genetic distance. The C78 primary core collection achieved an allele retention rate of 84.59%, with minimal genetic redundancy, effectively representing both the geographic origins and genetic diversity of the original accessions. These findings provide a robust foundation for the conservation of medicinal Polygonatum spp. germplasm and offer potential resources for future genetic improvement and variety selection.