Objective A concise collection of the highly popular Paris polyphylla germplasms was preliminarily established to aid the resource preservation and utilization.

Methods Genetic diversity of 60 P. polyphylla accessions was determined using 15 ISSR primers, population structure analyzed by Structure software, clustering classified by NTSYSpc2.10e, and principal components selected by PCA. Representatives of the 60 target germplasms were gathered using the grouping-proportional sampling method derived from the Structure analysis. The effectiveness of the collection in covering the genetic diversity of the P. polyphylla accessions was scrutinized.

Results The 15 ISSR primers amplified 102 loci with 97.05% polymorphic and high genetic diversity of average Shannon's information index (I) at 0.5022 and Nei's genetic diversity index (He) at 0.3328. The Structure analysis suggested that K=3 was the optimal number of subpopulations. The results obtained by the population structure analysis agreed with that by the principal coordinate analysis (PCoA) but differed slightly than the cluster analysis, which correlated with the geographic distribution. Using the grouping-proportional sampling method, 12 accessions selected by using 7 varied sampling rates represented 20% of the original germplasms. The collection retained the original I, He, and effective allele number (Ne) at a rate of 104.22%, 106.43%, and 107.71%, respectively. The t-test and the PCoA on the collection showed rich genetic diversity and uniform distribution in representing the 60 P. polyphylla accessions.

Conclusion The preliminarily established collection of P. polyphylla exhibited significant genetic diversity satisfactorily reflecting that of the 60 target germplasms.