Medicinal plants produce valuable secondary metabolites with anticancer, analgesic, anticholinergic or other activities, but low metabolite levels and limited available tissue restrict metabolite yields. Transformed root cultures, also called hairy roots, provide a feasible approach for producing valuable secondary metabolites. Various strategies have been used to enhance secondary metabolite production in hairy roots, including increasing substrate availability, regulating key biosynthetic genes, multigene engineering, combining genetic engineering and elicitation, using transcription factors (TFs), and introducing new genes. In this review, we focus on recent developments in hairy roots from medicinal plants, techniques to boost production of desired secondary metabolites, and the development of new technologies to study these metabolites. We also discuss recent trends, emerging applications, and future perspectives.

In the process of catalyzing carotenoids into various apocarotenoids and other derivatives, carotenoid cleavage dioxygenases (CCDs) play key roles. However, little information on CCDs has been reported in regard to Salvia miltiorrhiza. In this study, a total of 21 CCD genes were identified in the whole genome of S. miltiorrhiza, mainly distributed between five chromosomes. Phylogenetic relationship analysis revealed that 21 SmCCD genes were classified into four subfamilies, including SmCCD4, 7, 8, and NCED; the members of the same subfamily show similar gene structures and tertiary structures. The interspecific collinearity with other plant species, such as Arabidopsis thaliana and Oryza sativa was analyzed. Cis-elements analysis demonstrated that the majority were stress response-, light response-, growth-, and development-related. The expression pattern of the SmCCD genes was expressed in the analyzed tissues. Furthermore, the majority of the SmCCD4 subfamily members varied in their expression levels under the treatment of MeJA, YE, and ABA, indicating the potential function of SmCCD4 in the metabolism process of S. miltiorrhiza. In general, this study provides a systematic analysis of SmCCD genes and lays the foundation for uncovering the regulation and function of SmCCD genes in S. miltiorrhiza.