Identification of cold stress responsive microRNAs in two winter turnip rape (Brassica rapa L.) by high throughput sequencing

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.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1242-4) contains supplementary material, which is available to authorized users.

Transcriptome Arofile of Brassica rapa L. Reveals the Involvement of Jasmonic Acid, Ethylene, and Brassinosteroid Signaling Pathways in Clubroot Resistance

“…Analysis of gene expression was performed for all samples at 4, 8, 16, and 32 dpi of "85-74" with LAB-4. The expression levels of genes investigated in this study were calculated with the −∆∆Ct method [47], where ∆∆Ct = (CT gene − CT actin ) treat − (CT gene − CT actin ) control .…”

Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

“…Altered expression pro les of cold-regulated genes involved in lipid metabolism, chloroplast function, carbohydrate metabolism and free radical detoxi cation, observed in cold-sensitive Arabidopsis mutants, supports the suggestion that at least some cold-induced genes play a role in acclimation to cold temperatures (Abla et al 2019;Provart et al 2003). Zeng et al (Zeng et al 2018) studied cold stress responsive microRNAs in two winter turnip rape (Brassica rapa L.) by high throughput sequencing. The work indicated that miRNA and putative target genes mediated metabolic processes and stress responses are signi cant to cold tolerance in H. fulva.…”

“…The results showed that under cold stress, 376 miRNAs were differentially expressed in "Jinyan" leaves, while up to 90 miRNAs were up-regulated in "Jinyan" roots. The research shows that the cold tolerance of root is very important for the survival of Jinyan in winter (Zeng et al 2018). In order to determine the difference of miRNAs of the same variety of H. fulva under control and cold stress.…”

“…In order to determine the difference of miRNAs of the same variety of H. fulva under control and cold stress. It is known that the above ground part of "Jinyan" is more sensitive to cold stress, showing poor growth and aging (Zeng et al In 2018), the number of miRNAs differentially expressed in "Jinyan" leaves is relatively high, which may be related to the solution of "Jinyan" to alleviate cold induced damage such as ice induced cytoplasmic damage (Geyikoglu et al 2017). Previous studies have shown that small changes in miRNA expression can lead to signi cant changes in mRNA levels and related biological processes (Maddaly et al 2018).…”

Identification of MicroRNAs and Their Targets That Respond to Powdery Mildew Infection in Cucumber by Small RNA and Degradome Sequencing

“…The lengths of the novel miRNAs varied from 18 to 25 nt, with 24 nt being the predominant length (102/133). The minimum free energies of their pre-miRNA hairpin structures were −192.5 to −20.9 kcal • mol −1 with an average of −53.2 kcal • mol −1 , which corresponds to those of other plant miRNA precursors (Zeng et al, 2018). Csa-novel_12 was the most abundant novel miRNA with a TPM value of >52,000 in all 12 libraries.…”