College of Electrical and Information Engineering, Jilin Agricultural Science and Technology University, Jilin, Jilin, China.
College of Information and Control Engineering, Jilin Institute of Chemical Technology, Jilin, Jilin, China.
PLoS One. 2023 Aug 17;18(8):e0290163. doi: 10.1371/journal.pone.0290163. eCollection 2023.
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.
人参是一种珍贵的中草药，以其缓解某些疾病和促进整体健康的功效而闻名于世。在这项研究中，我们针对 13 种必需环境因素（包括空气温度、空气底层温度、地表平均温度、土壤温度、地表短波辐射、土壤水分、土壤含水量、降雨量、总降水量、海拔、土壤类型、土壤 pH 值和土壤水势）对必需皂苷积累的影响进行了加权基因共表达网络分析（WGCNA）。我们共鉴定出 40 个与典型环境因素和必需皂苷积累相关的转录模块。其中，18 个模块与典型环境因素的影响密切相关，而 22 个模块与必需皂苷的积累密切相关。这些结果通过检查转录组、皂苷含量、环境因子信息和已发表的数据得到了验证，并揭示了在必需环境因子影响下皂苷积累在转录组水平上的调控基础。我们提出了一个受典型环境因子影响的转录调控网络介导的皂苷积累工作模型。基于该模型构建了同构白盒神经网络，并对白盒神经网络的预测结果与皂苷积累进行了相关性分析。基于本研究获得的结果和已知影响皂苷 Rb1 生物合成的转录本进行的生物信息学分析验证了我们的关联导向图在预测皂苷含量方面的有效性。该有向图代表了一种有用的工具，可以在考虑人参和其他药用植物必需环境因素影响的情况下，操纵皂苷生物合成。
