Metabolome and transcriptome analyses identify the underground rhizome growth through the regulation of rhizome apices in Panax ginseng

Panax ginseng C. A. Mey. is a well-known oriental medicine as a stimulant and dietary supplement. The ginseng rhizome, as one of the principal medicinal organs, plays an important role in aboveground organ growth and root development, although no studies on ginseng rhizome growth have been recorded. In this study, we identified that shoot apical meristem (SAM) was included in the rhizome bud, which could regulate the underground rhizome growth of ginseng. In microscopic examination, ginseng SAM included the central zone, peripheral zone, rib zone, and organizing center; secondary root structures were observed in ginseng main roots and lateral roots; primary root structures were observed in ginseng fibrous roots; rhizome had a stem structure with pith and discontinuous cambium. The metabolites in different underground ginseng organs were identified using ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS), with oleanane (OA)-type ginsenosides accumulating primarily in the rhizome buds. In addition, ginseng rhizome buds contained a low level of 3-indoleacetonitrile (IAN, one type of auxin), a high amount of abscisic acid (ABA), and a high level of jasmonoyl-isoleucine (JA-Ile, active form of jasmonic acid). ABA and JA-Ile could drastically limit the shooting rate of ginseng embryonic calli, however IAN boosted the rooting rate. Furthermore, the expression of genes involved in ginsenoside biosynthesis, phytohormone production, and shoot stem cell regulatory pathways were studied. This is the first study of SAM in medicinal herbs, and we believe that the results may offer new information about the development of ginseng underground rhizomes.