Abstract
BackgroundMicroRNAs (miRNAs) have functions in diverse biological processes such as growth, signal transduction, disease resistance, and stress responses in plants. Thermotherapy is an effective approach for elimination of viruses from fruit trees. However, the role of miRNAs in this process remains elusive. Previously, we showed that high temperature treatment reduces the titers of Apple stem grooving virus (ASGV) from the tips of in vitro-grown Pyrus pyrifolia plants. In this study, we identified high temperature-altered pear miRNAs using the next generation sequencing technology, and futher molecularly characterized miRNA-mediated regulaton of target gene expression in the meristem tip and base tissues of in vitro-grown, ASGV-infected pear shoots under different temperatures.ResultsUsing in vitro-grown P. pyrifolia shoot meristem tips infected with ASGV, a total of 22,592,997 and 20,411,254 clean reads were obtained from Illumina high-throughput sequencing of small RNA libraries at 24 °C and 37 °C, respectively. We identified 149 conserved and 141 novel miRNAs. Seven conserved miRNAs and 77 novel miRNAs were differentially expressed at different temperatures. Target genes for differentially expressed known and novel miRNAs were predicted and functionally annotated. Gene Ontology (GO) analysis showed that high-ranking miRNA target genes were involved in metabolic processes, responses to stress, and signaling, indicating that these high temperature-responsive miRNAs have functions in diverse gene regulatory networks. Spatial expression patterns of the miRNAs and their target genes were found to be expressed in shoot tip and base tissues by qRT-PCR. In addition, high temperature reduced viral titers in the shoot meristem tip, while negatively regulated miRNA-mediated target genes related to resistance disease defense and hormone signal transduction pathway were up-regulated in the P. pyrifolia shoot tip in response to high temperature. These results suggested that miRNAs may have important functions in the high temperature-dependent decrease of ASGV titer in in vitro-grown pear shoots.ConclusionsThis is the first report of miRNAs differentially expressed at 24 °C and 37 °C in the meristem tip of pear shoots infected with ASGV. The results of this study provide valuable information for further exploration of the function of high temperature-altered miRNAs in suppressing viral infections in pear and other fruit trees.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2126-8) contains supplementary material, which is available to authorized users.
Highlights
MicroRNAs have functions in diverse biological processes such as growth, signal transduction, disease resistance, and stress responses in plants
Liu et al BMC Genomics (2015) 16:945 (Continued from previous page). This is the first report of miRNAs differentially expressed at 24 °C and 37 °C in the meristem tip of pear shoots infected with Apple stem grooving virus (ASGV)
Analysis of small RNAs from in vitro-cultured pear shoots infected with ASGV in response to high temperature To identity miRNAs associated with high temperature treatment, small RNA differential expression libraries were constructed from 24 °C- and 37 °C-treated in vitrogrown pear shoots infected with ASGV and sequenced using high-throughput Solexa sequencing
Summary
MicroRNAs (miRNAs) have functions in diverse biological processes such as growth, signal transduction, disease resistance, and stress responses in plants. MiRNAs species usually negatively regulate their target genes via translational inhibition or cleavage of target mRNAs and play a pivotal role in a wide variety of biological processes such as plant development, signal transduction, resistance pathways, as well as abiotic and biotic stresses [12,13,14,15,16]. As AGO1 protein is a central component of the RISC in the miRNAs/siRNAs-mediated post-transcriptional gene silencing (PTGS) pathways [25], these findings suggest the possible role of miRNA in regulating the innate antiviral silencing pathways in plants
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