Multi-dimensional identification and quality evaluation of Paris polyphylla cultivated populations using morphological, molecular, cytological and metabolic traits
Introduction Paris polyphylla is an endangered medicinal herb valued for its steroidal saponins, yet the phenotypic stability, genetic diversity, and quality differentiation of cultivated populations remain insufficiently understood. Methods In this study, 28 representative populations from Yunnan Province were evaluated under common-garden conditions using morphological, molecular, cytogenetic, genomic and phytochemical analyses. Results The populations showed generally synchronized phenological development but differed significantly in several agronomic traits. DNA barcoding based on ITS and trnL–trnF sequences achieved high amplification and sequencing success. Among the representative sequences examined, ITS exhibited greater haplotype richness and sequence variation than trnL–trnF. However, because each population was represented by only one consensus sequence, within-population variation and a conventional DNA barcode gap could not be evaluated. Flow cytometry and chromosome counting confirmed that all populations were diploid, although substantial variation in genome size and karyotype characteristics was observed. HPLC analysis further revealed marked differences in steroidal saponin composition and content among populations.Correlation analyses linked saponin variation to multiple agronomic traits, karyotypic features, and genome size. Exploratory partial least squares path modeling showed that temperature was positively associated with plant growth, whereas plant growth was negatively associated with the composite saponin profile. The model explained a limited proportion of the variation in the endogenous constructs, and the identified paths were interpreted as statistical associations rather than causal effects. Discussion Overall, this study clarifies the genetic and ecological drivers of saponin variation in cultivated P. polyphylla, providing an integrated framework for germplasm identification, quality evaluation, and sustainable utilization of cultivated resources.