Microrna-guided regulation of heat stress response in wheat

Citation

Ravichandran, S., Ragupathy, R., Edwards, T., Domaratzki, M., Cloutier, S. (2019). Microrna-guided regulation of heat stress response in wheat. BMC Genomics, [online] 20(1), http://dx.doi.org/10.1186/s12864-019-5799-6

Plain language summary

With rising global temperatures, understanding plants’ adaptation to heat stress is becoming more important than ever before. The land areas for the cultivation of crops in the next few decades will be increasingly dictated by their geographical adaptation to the rapidly evolving environmental conditions. Epigenetics refers to the study of changes caused by modification of gene expression that do not involve changes in the underlying DNA sequence. Increasing knowledge of this field of study combined with the rapid development of next generation sequencing methods have led to many discoveries linking epigenetics mechanisms to stress adaptation. Here, we exposed wheat plants to a 5-day heat stress just prior to the onset of flowering, a critical developmental time, and we compared them to unstressed plants. To do so, we sampled leaf tissue and extracted total RNA from heat-stressed and unstressed plants immediately at the end of the stress, one day and four days later. Three types of RNA were studied: micorRNA (miRNA), degraded RNA and messenger RNA (gene-coding mRNA). miRNAs are small RNA molecules that have the ability to regulate gene expression because, in conjunction with some enzymes, they will cut their gene targets. The degraded RNA sequences identify the genes that have been cut as a consequence of the binding between miRNA and mRNA molecules. Deep sequencing of these RNA libraries was performed and hundreds of millions of sequences were obtained, processed and analyzed. Through the extensive analyses of these three datasets, we were able to identify specific miRNAs that are either up or down-regulated upon heat stress and to determine, in turn, the specific target gene or genes whose expression was modulated upon heat stress and during the recovery period. The phenomenon is termed miRNA-guided post-transcriptional gene regulation. The miRNAs and their targets identified in this study could be capitalized upon to develop new wheat breeding strategies to improve heat stress tolerance in wheat.

Abstract

Background: With rising global temperature, understanding plants' adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the post-transcriptional level. In this study, small RNAs and the degradome (parallel analysis of RNA ends) of leaf tissues collected from control and heat-stressed wheat plants immediately at the end of the stress period and 1 and 4 days later were analysed. Results: Sequencing of 24 small RNA libraries produced 55.2 M reads while 404 M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. Heat stress responsive miRNA targeted superoxide dismutases and an array of homeobox leucine-zipper proteins, F-box proteins and protein kinases. Query of miRNA targets to interactome databases revealed a predominant association of stress responses such as signalling, antioxidant activity and ubiquitination to superoxide dismutases, F-box proteins, pentatricopeptide repeat-containing proteins and mitochondrial transcription termination factor-like proteins. Conclusion: The interlaced data set generated in this study identified and validated heat stress regulated miRNAs and their target genes associated with thermotolerance. Such accurate identification and validation of miRNAs and their target genes are essential to develop novel regulatory gene-based breeding strategies.

Publication date

2019-06-13

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