Abstract:In order to understand the correlation between characters of single nucleotide polymorphism (SNP) of internal transcribed spacer (ITS) sequences and composition of steroidal saponins of Paris polyphylla var. yunnanensis, the effect of SNP on the quality stability of medicinal materials, the ITS sequences of 37 samples were compared by MegAlign, and then classified according to SNP loci. In addition, 7 steroidal saponins (polyphyllin Ⅰ, Ⅱ, Ⅴ, Ⅵ, Ⅶ, H, dioscin) in samples were determined by HPLC-DAD. The steroidal saponin composition characteristics of each genotype were statistical analysis by SPSS 25.0 & SIMCA-P 15.0. The results showed that there were 40 double-allelic polymorphic sites in ITS sequences of P. polyphylla var. yunnanensis, including 32 base conversion sites and 8 base inversion sites. According to SNP characteristics, 37 samples were divided into two genotypes: YN-I and YN-II. Six kinds of steroidal saponins (polyphyllin Ⅰ, Ⅱ, Ⅵ, Ⅶ, H, dioscin) were widely distributed in samples, while polyphyllin Ⅴ was relatively rare. The mean total content of pharmacopoeia index components in YN-I and YN-II were 1.070% and 0.93%, which the sample pass rate were 68.42% and 77.78%, respectively. The mean total content of 7 steroidal saponins were 1.65% and 1.32%, respectively. ANOVA analysis showed that there was significant differentiation of steroidal saponins profile between two genotypes, while there was no significant difference in the index components of pharmacopoeia, so the medicinal value of two genotypes should be equivalent. Cluster analysis (CA) and principal component analysis (PCA) showed the dispersion of YN-I was higher than that of YN-II, indicating the quality of medicinal materials of YN-II was more stable and the individual differences in steroidal saponins synthesis and accumulation in YN-II was smaller than YN-I. Therefore, the SNP characteristics of YN-II were of great significance for the screen of molecular genetic markers in the breeding of Paris polyphylla var. yunnanensis.