Abstract
BackgroundOilseed rape is an excellent candidate for phytoremediation of cadmium (Cd) 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 to infer Cd-induced regulation has not been reported in B. napus.ResultsWe 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. Cd treatment significantly affected the expression of 22 miRNAs belonging to 11 families in the root and 29 miRNAs belonging to 14 miRNA families in the shoot. Five miRNA families (MIR395, MIR397, MIR398, MIR408 and MIR858) and three novel miRNAs were differentially expressed in both tissues. A total of 399 differentially expressed genes (DEGs) in the root and 389 DEGs in the shoot were identified, with very little overlap between tissue types. Eight anti-regulation miRNA-mRNA interaction pairs in the root and eight in the shoot were identified in response to Cd and were involved in key plant stress response pathways: for example, four genes targeted by miR398 were involved in a pathway for detoxification of superoxide radicals. Cd stress significantly impacted the photosynthetic pathway. Transcription factor activation, antioxidant response pathways and secondary metabolic processes such as glutathione (GSH) and phenylpropanoid metabolism were identified as major components for Cd-induced response in both roots and shoots.ConclusionsCombined miRNA and mRNA profiling revealed miRNAs, genes and pathways involved in Cd response which are potentially critical for adaptation to Cd stress in B. napus. Close crosstalk between several Cd-induced miRNAs and mRNAs was identified, shedding light on possible mechanisms for response to Cd stress in underground and aboveground tissues in B. napus. The pathways, genes, and miRNAs identified here will be valuable targets for future improvement of cadmium tolerance in B. napus.
Highlights
Oilseed rape is an excellent candidate for phytoremediation of cadmium (Cd) 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
Our results showed that the quantitative real-time RT-PCR (qRT-PCR) analysis for 13 of the 15 differentially expressed mRNAs and seven of the ten differentially expressed miRNAs displayed similar expression patterns to those generated from high-throughput sequencing (Additional file 2: Figure S1), confirming the reliability of the data provided by Ribonucleic acid (RNA)-Seq
The expression of a range of miRNAs were changed under cd stress in oilseed rape Zhou et al (2012) previously identified eight miRNA families differentially expressed in response to Cd stress in B. napus roots, and 13 miRNA families differentially expressed in response to Cd stress in B. napus shoots [35]
Summary
Oilseed rape is an excellent candidate for phytoremediation of cadmium (Cd) 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. Plants have evolved a range of mechanisms for heavy metal detoxification, including pumping heavy metals out of the plasma membrane, chelation, and binding to various thiol compounds in the cytosol followed by sequestration into vacuoles [8,9,10]. Glutathione (GSH) is a well documented and highly essential component for Cd detoxification [12], and GSH- or phytochelatin (PC)-conjugated vacuolar sequestration is one of the most important mechanisms of Cd accumulation and tolerance in plants [13,14,15]. Cd-responsive miRNAs have been identified in rice (Oryza spp.) [25, 26], narrowleaf cattail (Typha angustifolia) [27], Medicago truncatula [28], and radish (Raphanus spp.) [29], strongly supporting miRNAs as key post-transcriptional regulators of Cd stress responses in plants [30]
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