Abstract
Background/Objectives: Rehmannia glutinosa, a highly valuable medicinal plant in China, is encountering severe replant disease. Replant disease represents a complex stress driven by multiple principal factors (RDFs), including allelochemicals, microbes, and their interactions. miRNAs are recognized as key regulators of plant response to stresses; however, their specific roles within RDFs are not entirely clear. Methods: This study builds six RDF treatments, comprising R. glutinosa continuously planted (SP), normally planted (NP), and NP treated with ferulic acid (FA), Fusarium oxysporum (FO), and a combination of FA with FO (FAFO). sRNA-seq technology was used to identify crucial miRNAs in response to diverse RDFs. Results: In total, 30 sRNA datasets were generated from the SP, NP, FA, FO, and FAFO samples. A total of 160 known and 41 novel miRNAs (RgmiRNAs) were identified in the R. glutinosa genome based on the sRNA database. Abundance analysis revealed that RgmiRNAs in SP exhibited a distinct expression profile in comparison with others. Of these, 124, 86, 86, and 90 RgmiRNAs were differentially expressed in SP, FA, FO, and FAFO compared with NP. Target analysis indicated that RgmiRNAs downregulated in both SP and RDFs impede the organism growth of R. glutinosa. RgmiRNAs upregulated in SP can disrupt root formation and nutrient metabolism, in which, two RgmiR398 were uniquely expressed in SP. It was confirmed to target RgCSD genes. The expression patterns of RgmiR398 and RgCSD indicated that replant disease induces the oxidative damage of R. glutinosa through RgmiR398. Conclusions:RgmiRNA profiling under RDFs provides a theoretical basis for the further clarification of RgmiRNA function in replant disease.