Objective This study employed combined ISSR-SCoT markers with UPGMA and Euclidean metric clustering to analyze genetic diversity among 24 Polygonatum accessions from diverse origins, facilitating germplasm conservation and utilization.

Method Using ISSR and SCoT molecular marker technology, the genetic diversity of Polygonatum from 24 provenances in 11 provinces was analyzed.

Result 15 primers were selected from ISSR and SCoT universal primers, respectively. 229 (ISSR) and 210 (SCoT) clear band markers were obtained after amplification. The average polymorphism percentage was 98.40% (ISSR) and 98.10% (SCoT), respectively. ISSR molecular marker technology could obtain more polymorphic sites. Nei's gene differentiation coefficient (G_st) of 24 Polygonatum was 0.0474, indicating that 95.26% of the genetic variation was intraspecific, and the gene flow N_m > 1 indicated significant gene flow within the species. 15 P. sibiricum Red. germplasm resources had a G_st of 0.0471, indicating that 95.29% of the genetic variation was intraspecific. N_m > 1 indicated more intraspecific gene exchange. UPGMA analysis of the ISSR, SCoT and ISSR-SCoT combined data showed that the clustering results of the three types of data had similarities and differences. In this study, the ISSR-SCoT combined data were further clustered using the Euclidean metric, and consistent with the results of the UPGMA clustering analysis, ZJ6 and HN4 had the closest genetic distances, and the results were basically same as the Euclidean metric algorithm clustering results by visualizing the genetic coefficients of 24 Polygonatum in a clustered heatmap.

Conclusion The joint use of ISSR and SCoT molecular markers and the combined application of UPGMA and Euclidean metric algorithms can provide more comprehensive information on the genetic diversity of Polygonatum. The 24 cultivated germplasm resources of Polygonatum from different origins had rich genetic diversity and were highly correlated with geographical locations.