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Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV

ABSTRACT: Understanding of plant adaptation to abiotic stresses has implications in plant breeding, especially in the context of climate change. MicroRNAs (miRNAs) and short interfering RNAs play a crucial role in gene regulation. Here, wheat plants were exposed to one of the following stresses: continuous light, heat or ultraviolet radiations over five consecutive days and, leaf tissues from three biological replicates were harvested at 0, 1, 2, 3, 7 and 10 days after treatment (DAT). A total of 72 small RNA libraries were sequenced on the Illumina platform generating ~524 million reads corresponding to ~129 million distinct tags from which 232 conserved miRNAs were identified. The expression levels of 1, 2 and 79 miRNAs were affected by ultraviolet radiations, continuous light and heat, respectively. Approximately 55% of the differentially expressed miRNAs were downregulated at 0 and 1 DAT including miR398, miR528 and miR156 that control mRNAs involved in activation of signal transduction pathways and flowering. Other putative targets included histone variants and methyltransferases. These results suggest a temporal miRNA-guided post-transcriptional regulation that enables wheat to respond to abiotic stresses, particularly heat. Designing novel wheat breeding strategies such as regulatory gene-based marker assisted selection depends on accurate identification of stress induced miRNAs.

ORGANISM(S): Triticum aestivum

PROVIDER: GSE83738 | GEO | 2017/01/17

SECONDARY ACCESSION(S): PRJNA326902

REPOSITORIES: GEO

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Project description:Purpose: To identify abiotic stress responsive and tissue specific miRNAs at genome wide level in wheat (Triticum aestivum) Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. Using UEA sRNA workbench we identified 47 conserved miRNAs belonging to 20 families, 1030 candidate novel and 51 true novel miRNAs. Several of these miRNAs displayed tissue specific expression whereas few were found to be responsive to abiotic stress treatments. Target genes were predicted for miRNAs identified in this study and their grouping into functional categories revealed that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three conserved miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by corresponding miRNAs. Expression profiling of confirmed target genes of these miRNAs was also performed. Conclusions: This is the first comprehensive study on profiling of miRNAs in a variety of tissues and in response to several abiotic stresses in wheat. Our findings provide valuable resource for better understanding on the role of miRNAs in stress tolerance as well as plant development. Additionally, this information could be utilized for designing wheat plants for enhanced abiotic stress tolerance and higher productivity. Total eight (three stress, one control and four tissue specific small RNA libraries were pepared and sequenced independently [wheat control (WC), wheat high temperature stressed (WHTS), wheat salinity stressed (WSS) and wheat drought stressed (WDS), wheat shoot(WSH), wheat leaf (WLF), wheat flower(WFL), wheat root(WRT)] on Illumina GAIIx

Project description:Arabidopsis microRNA expression regulation was studied in a wide array of abiotic stresses such as drought, heat, salinity, copper excess/deficiency, cadmium excess and sulphur deficiency. A home-built RT-qPCR mirEX platform for the amplification of 289 Arabidopsis microRNA transcripts was used to study their response to abiotic stresses. Small RNA sequencing and Northern hybridization were performed to study the expression of mature microRNAs. In the case of common climate change related stresses such as drought, heat and salinity we observed broad induction of the level of primary miRNAs that was not observed at the level of microRNAs.. In the case of local soil pollution stresses, that are represented by heavy metal contaminations or deprivation of a specific micro- or macroelement, the transcriptional response of pri-miRNAs was quite limited but also not predictive to the level of the mature microRNA. This points to an essential role of posttranscriptional regulation of microRNAs expression. We found that the level of several microRNAs can be differentially regulated in early and late response to stress. New Arabidopsis microRNAs responsive to abiotic stresses were discovered. Three microRNAs: miR319a/b, miR319b.2, and miR400 have been found to be responsive in several abiotic stresses and thus can be regarded as a general stress-responsive microRNA species. Additionally, a new target for miR319b.2 – TBL10 has been experimentally confirmed. However, its level under different abiotic stresses is unchanged in comparison to control conditions. In the promoter region of the TBL10 gene we found the presence of many stress-responsive elements. We suggest that transcriptional induction resulting in the increase of transcript levels is downregulated by the increase of the miR319b.2 ultimately resulting in a stable level of TBL10 mRNA. Our experiments show the existence of a complex regulatory network involved in the microRNA level control that is necessary to fine-tune plant response to environmental cues.

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Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV

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