Transcriptomics and metabolomics of the molecular mechanisms of ginseng's response to the continuous cropping obstacle

Ginseng is a plant with a long history of use in traditional Chinese medicine. However, large-scale cultivation of ginseng is limited by widespread issues with continuous cropping. To explore the physiological and molecular mechanisms behind ginseng crop disorders, transcriptomics and metabolomics were combined in this study to analyze the effects of continuous cropping on changes in ginseng metabolites, differential gene expression, and regulation of root secretions. The results showed that 106 metabolites and 1175 genes were significantly altered at the metabolic and transcriptional levels in ginseng from continuous cropping compared with the control group. More organic acids, alkaloids, flavonoids, and phenolics accumulated in the ginseng from continuous cropping than the control ginseng. Furthermore, significant differences were found in the expression of genes involved in phytohormone signaling, phenylpropanoid biosynthesis, and plant–pathogen interaction pathways. The results provide information on the regulation of expression of genes associated with continuous cropping disorders, and suggest that continuous cropping disorders may lead to severe damage to ginseng roots by pathogens and result in slow growth. Our research provides new insight into the response of ginseng to crop disorders, and reveals potential molecular mechanisms of the ginseng response to crop disorders. •Continuous cropping of ginseng seriously affects its growth and development.•Changes were observed in 106 metabolites after continuous cropping of ginseng.•Continuous cropping ginseng showed significant changes in 1175 genes at the transcriptional level.•There are significant differences in gene expression in plant hormone signal transduction, phenylpropanoid biosynthesis pathways.