Continuous cropping (CC) is a common practice in agriculture, and usually causes serious economic losses due to soil degeneration, decreased crop yield and quality, and increased disease incidence, especially in medicinal plants. Continuous cropping obstacles (CCOs) are mainly due to changes in soil microbial communities, nutrient availability, and allelopathic effects. Recently, progressive studies have illustrated the molecular mechanisms of CCOs, and valid strategies to overcome them. Transcriptomic and metabolomics analyses revealed that identified DEGs (differently expressed genes) and metabolites involved in the response to CCOs are involved in various biological processes, including photosynthesis, carbon metabolism, secondary metabolite biosynthesis, and bioactive compounds. Soil improvement is an effective strategy to overcome this problem. Soil amendments can improve the microbial community by increasing the abundance of beneficial microorganisms, soil fertility, and nutrient availability. In this review, we sum up the recent status of the research on CCOs in medicinal plants, the combination of transcriptomic and metabolomics studies, and related control strategies, including uses of soil amendments, crop rotation, and intercropping. Finally, we propose future research trends for understanding CCOs, and strategies to overcome these obstacles and promote sustainable agriculture practices in medicinal plants.

Soil salinity represents a significant abiotic constraint limiting the productivity and geographical expansion of rapeseed (Brassica napus L.), yet the coordination among the signaling, hormonal, metabolic, and regulatory layers underlying salt tolerance remains incompletely understood. This study elucidates the physiological, biochemical, and transcriptomic responses of B. napus inbred line 383-5 to moderate salt stress (100 mM NaCl at day 10), identifying key lncRNA–mRNA regulatory networks. Salt stress induced pronounced, dose-dependent growth inhibition, oxidative damage, and osmotic adjustment, accompanied by extensive transcriptional reprogramming. Genome-wide analyses identified 6215 differentially expressed protein-coding genes and 941 salt-responsive long non-coding RNAs (lncRNAs), revealing coordinated regulation of ion transport, redox homeostasis, phytohormone signaling, and secondary metabolism. Functional enrichment analyses highlighted the central involvement of abscisic acid and ethylene signaling pathways, MAPK cascades, membrane transporters, and antioxidant systems. Notably, salt stress strongly activated the phenylpropanoid and lignin biosynthesis pathways, suggesting reinforced cell wall remodeling and enhanced oxidative stress mitigation. Integration of lncRNA–mRNA regulatory networks further indicated that non-coding transcripts act as important modulators linking hormone signaling, redox balance, and metabolic adaptation. Collectively, these results reveal a multilayered and tightly synchronized regulatory framework underlying salinity tolerance in B. napus and provide valuable molecular targets for the genetic improvement of salt-resilient rapeseed cultivars.