MicroRNAs-mRNAs Expression Profile and Their Potential Role in Cadmium Stress Response in Brassica napus

Abstract Background: Oilseed rape is an excellent candidate for phytoremediation of cadmium-contaminated soils given its advantages of high biomass, fast growth, moderate metal accumulation, ease of harvesting, and metal tolerance, but the cadmium response pathways in this species (Brassica napus) have yet to be fully elucidated. A combined analysis of miRNA and mRNA expression data to infer Cd-induced transcriptional regulation has not been previously been reported in B. napus. Results: In the current study, we characterized concurrent changes in miRNA and mRNA profiles in the roots and shoots of B. napus seedlings after 10 days of 10 mg/L Cd2+ treatment. In total, 39 miRNAs belonging to 14 families were identified in the root, and 53 miRNAs belonging 16 miRNA families were identified in the shoot, of which the miR397, miR395, miR408, miR398 and miR858 families showed the most significant expression changes in response to Cd stress. A further 399 in the root and 389 differentially expressed genes (DEGs) in the shoot were identified, with very little overlap between tissue types. A total of 24 root and 16 shoot anti-regulation miRNA-mRNA interaction pairs (up-regulation of miRNA and down-regulation of mRNA or vice-versa) were identified in response to Cd, which involved in the key pathways of palnt stress response, e.g. four genes targeted by one miRNA were involved in a pathway for detoxification of superoxide radicals. Cd stress significantly impacted the photosynthetic pathway. We identified transcription factor activation, antioxidant response pathways and secondary metabolic processes such as glutathione (GSH) and phenylpropanoid metabolism as major components in the response to Cd-induced stress in both roots and shoots. Conclusions: miRNAs and mRNAs showed concurrent expression changes for cadmium response in Brassica napus. The leaves and roots showed several overlap of differentially expressed miRNAs but very little overlap of differentially expressed mRNAs for Cd response. Several anti-regulation miRNA-mRNA interaction pairs were identified, which involved in the key pathways of plant stress response like detoxification of superoxide radicals. Photosynthetic pathway, transcription factor activation, antioxidant response and secondary metabolic processes were major components for cadmium response.