Abstract
BackgroundLow temperature is a major abiotic stress affecting the production of rapeseed in China by impeding plant growth and development. A comprehensive knowledge of small-RNA expression pattern in Brassica rapa under cold stress could improve our knowledge of microRNA-mediated stress responses.ResultsA total of 353 cold-responsive miRNAs, 84 putative novel and 269 conserved miRNAs, were identified from the leaves and roots of two winter turnip rape varieties ‘Longyou 7’ (cold-tolerant) and ‘Tianyou 4’ (cold-sensitive), which were stressed under − 4 °C for 8 h. Eight conserved (miR166h-3p-1, miR398b-3p, miR398b-3p-1, miR408d, miR156a-5p, miR396h, miR845a-1, miR166u) and two novel miRNAs (Bra-novel-miR3153-5p and Bra-novel-miR3172-5p) were differentially expressed in leaves of ‘Longyou 7’ under cold stress. Bra-novel-miR3936-5p was up-regulated in roots of ‘Longyou 7’ under cold stress. Four and five conserved miRNAs were differentially expressed in leaves and roots of ‘Tianyou 4’ after cold stress. Besides, we found two conserved miRNAs (miR319e and miR166m-2) were down-regulated in non-stressed roots of ‘Longyou 7’ compared with ‘Tianyou 4’. After cold stress, we found two and eight miRNAs were differentially expressed in leaves and roots of ‘Longyou 7’ compared with ‘Tianyou 4’. The differentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR166 and miR319 families. A total of 211 target genes for 15 known miRNAs and two novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Five differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR, and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR166e, miR319, and Bra-novel-miR3936-5p) may play important roles in plant response to cold stress.ConclusionsOur work indicates that miRNA and putative target genes mediated metabolic processes and stress responses are significant to cold tolerance in B. rapa.
Highlights
Low temperature is a major abiotic stress affecting the production of rapeseed in China by impeding plant growth and development
Pre-miRNAs are sequentially processed by Dicer-like proteins in cell nucleus [11] and transferred to cytoplasm before assembled to RNA-induced silencing complexes (RISCs), which combine with Argonaute proteins
The degree of cold tolerance was estimated by measuring MDA content and POD activity, which were significantly increased in the leaves and roots of the two varieties under cold stress (Fig. 1)
Summary
Low temperature is a major abiotic stress affecting the production of rapeseed in China by impeding plant growth and development. A comprehensive knowledge of small-RNA expression pattern in Brassica rapa under cold stress could improve our knowledge of microRNA-mediated stress responses. The TFs combine with cis-acting elements to promote and regulate the transcription and expression of target genes, thereby improving the cold-tolerance capability of plants [7, 8]. MicroRNAs have been recently reported as new regulator in plant adaptation to environmental stresses [9, 10], which are small (20–24 nt), endogenous, and noncoding RNAs originate from 70 to 80 nt pre-miRNAs with stemloop structures. Many miRNAs related to cold tolerance, such as miR156, miR166, miR172,miR319, miR396, and miR397, are identified in plants with capability of regulating cold stress responses [24,25,26,27]. MiRNA related to cold stress is in need to be identified in Brassica, which is of great economic value in edible vegetable and oil production
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