Correlation coefficient, significance level, and corresponding sample scatter plot of transcripts closely associated with Rb1 and different modules.

Correlation coefficient, significance level, and corresponding sample scatter plot of transcripts closely associated with Rb1 and different modules.</p

Module-environment factors relationships.

Ginseng, a valuable Chinese medicinal herb, is renowned worldwide for its effectiveness in alleviating certain conditions and promoting overall health. In this study, we performed weighted gene co-expression network analysis (WGCNA) on the accumulation of essential saponins under the influence of 13 essential environmental factors (including air temperature, air bottom temperature, surface mean temperature, soil temperature, surface shortwave radiation, soil moisture, soil water content, rainfall, total precipitation, elevation, soil type, soil pH, and soil water potential). We identified a total of 40 transcript modules associated with typical environmental factors and the accumulation of essential saponins. Among these, 18 modules were closely related to the influence of typical environmental factors, whereas 22 modules were closely related to the accumulation of essential saponins. These results were verified by examining the transcriptome, saponin contents, environmental factor information and the published data and revealed the regulatory basis of saponin accumulation at the transcriptome level under the influence of essential environmental factors. We proposed a working model of saponin accumulation mediated by the transcriptional regulatory network that is affected by typical environmental factors. An isomorphic white-box neural network was constructed based on this model and the predicted results of the white-box neural network correlated with saponin accumulation. The effectiveness of our correlation-directed graph in predicting saponin contents was verified by bioinformatics analysis based on results obtained in this study and transcripts known to affect the biosynthesis of saponin Rb1. The directed graph represents a useful tool for manipulating saponin biosynthesis while considering the influence of essential environmental factors in ginseng and other medicinal plants.</div

Association diagram of ecological factors, saponin profiles, and TCEMs.

(A) Correlations of ecological factors and essential saponins with TCEMs. (B) Correlations among ecological factors, essential saponins, and grouped TCEMs.</p

Module-saponins trait associations for saponin Rb2 mainly.

Module-saponins trait associations for saponin Rb2 mainly.</p

The correlation coefficient, significance level, and corresponding sample scatter plot between modules and saponins.

The correlation coefficient, significance level, and corresponding sample scatter plot between modules and saponins.</p

Comparison of predicted (predict) values with reference (ref) values.

Comparison of predicted (predict) values with reference (ref) values.</p

Scatter plot of gene significance for Rb1 versus module membership in module ME57.

Scatter plot of gene significance for Rb1 versus module membership in module ME57.</p

Transcripts closely associated with Rb1 and different modules.

Transcripts closely associated with Rb1 and different modules.</p

Validity of saponin biosynthesis determined by the chi-square test.

Validity of saponin biosynthesis determined by the chi-square test.</p

Accurate transcript quantification from RNA-Seq data.

Accurate transcript quantification from RNA-Seq data.</p