Objective Due to the increasing market demand for Paris polyphylla, the resource supply cannot meet the demand, leading to over-exploitation of wild resources and genetic admixture. To address this issue, we aimed to construct an initial core germplasm collection to provide theoretical support for gene mining, germplasm improvement, and conservation.

Methods Genetic diversity analysis was conducted using 15 ISSR primers on 60 accessions. Population structure analysis was performed using Structure software, cluster analysis using NTSYSpc2.10e software, and principal component analysis (PCA) for validation. An initial core germplasm was constructed based on the grouping-proportional sampling method derived from Structure analysis, and its effectiveness was evaluated.

Results The 15 ISSR primers amplified a total of 102 loci, with a polymorphic locus rate of 97.05%. The average Shannon's information index (I) and Nei's genetic diversity index (He) were 0.5022 and 0.3328, respectively, indicating rich genetic diversity within the germplasm. Structure analysis suggested that K = 3 was the optimal number of subpopulations. Principal coordinate analysis (PCoA) results were consistent with population structure analysis, although cluster analysis showed slight differences, which were correlated with geographic distribution. Using the grouping-proportional sampling method, 12 accessions were selected from seven different sampling proportions, representing 20% of the original germplasm. The retention rates of Shannon's information index (I), Nei's genetic diversity index (He), and effective allele number (Ne) in the core germplasm were 104.22%, 106.43%, and 107.71%, respectively. The t-test and principal coordinate analysis (PCoA) demonstrated that the constructed core germplasm not only exhibits rich genetic diversity but also shows a uniform distribution within the original germplasm collection.

Conclusion Paris polyphylla exhibits significant genetic diversity, and the constructed initial core germplasm effectively represents the genetic diversity of the original germplasm.