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

Citation

Ragupathy, R., Ravichandran, S., Mahdi, M.S.R., Huang, D., Reimer, E., Domaratzki, M., Cloutier, S. (2016). Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV, 6 http://dx.doi.org/10.1038/srep39373

Plain language summary

Climate change translates to rising global temperatures, unprecedented carbon dioxide levels, more frequent droughts or heavy rainfalls and, in general, more unpredictable weather. From a plant perspective, it means increased exposure to abiotic stresses of greater magnitude. Heat, constant light and exposure to ultraviolet radiation are three abiotic stresses affecting plant growth. Small RiboNucleic Acids (RNAs) are small molecules that do not code for a protein but that nevertheless play a role in stress adaptation. Micro RNAs are only 21 to 24 nucleotides long but they have the ability to reduce the expression of entire networks of genes by binding to complementary messenger RNA molecules and inducing their cleavage before they get translated into proteins. Here, we exposed wheat plants to heat, constant light and UV stresses for a period of 5 days and extracted RNA immediately at the end of the stress period and at several time points during the 10-day recovery period. Micro RNA expression is greatly affected by heat stress but plays a minor role in plant adaptation to constant light and UV stresses. A total of 79 micro RNAs were differentially expressed immediately after heat exposure and during the early recovery period but only minor differences in expression were observed once the plants had recovered. Putative target genes of the differentially expressed micro RNAs include genes involved in determining flowering time for example. It is paramount to precisely identify the micro RNAs involved and their target genes if we want to design novel strategies for plants to cope with abiotic stresses.

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 radiation, 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.