Abstract
BackgroundMicroRNAs (miRNAs) are small RNA molecules that play important regulatory roles in plant development and stress responses. Identification of stress-regulated miRNAs is crucial for understanding how plants respond to environmental stimuli. Abiotic stresses are one of the major factors that limit crop growth and yield. Whereas abiotic stress-regulated miRNAs have been identified in vegetative tissues in several plants, they are not well studied in reproductive tissues such as inflorescences.ResultsWe used Illumina deep sequencing technology to sequence four small RNA libraries that were constructed from the inflorescences of rice plants that were grown under control condition and drought, cold, or salt stress. We identified 227 miRNAs that belong to 127 families, including 70 miRNAs that are not present in the miRBase. We validated 62 miRNAs (including 10 novel miRNAs) using published small RNA expression data in DCL1, DCL3, and RDR2 RNAi lines and confirmed 210 targets from 86 miRNAs using published degradome data. By comparing the expression levels of miRNAs, we identified 18, 15, and 10 miRNAs that were regulated by drought, cold and salt stress conditions, respectively. In addition, we identified 80 candidate miRNAs that originated from transposable elements or repeats, especially miniature inverted-repeat elements (MITEs).ConclusionWe discovered novel miRNAs and stress-regulated miRNAs that may play critical roles in stress response in rice inflorescences. Transposable elements or repeats, especially MITEs, are rich sources for miRNA origination.
Highlights
MicroRNAs are small RNA molecules that play important regulatory roles in plant development and stress responses
Plant miRNAs recognize their targets through near-perfect complementarity to direct RNA-Induced Silencing Complex (RISC)-mediated cleavage, in some cases translational inhibition and DNA methylation can be the mode of action of miRNA-mediated gene silencing [19,20,21]
Identification of miRNAs We constructed and sequenced four small RNA libraries using the inflorescences of rice plants that grew under control and three abiotic stress treatments
Summary
MicroRNAs (miRNAs) are small RNA molecules that play important regulatory roles in plant development and stress responses. SiRNAs are derived from double stranded RNA precursors and can be further divided into heterochromatic siRNAs (hc-siRNAs), trans-acting siRNAs (ta-siRNAs), long siRNAs (lsiRNAs), and natural processed by DCL proteins into sRNAs that target the antisense gene for regulation [13,14,15]. MiRNAs are distinguished from siRNAs since they are transcribed into a single-stranded pri-miRNA by RNA polymerase II, which folds into a stable, usually imperfect, hairpin structure [16]. This structure is processed by DCL1 to produce ~21 nt, double-stranded RNA duplex. Plant miRNAs recognize their targets through near-perfect complementarity to direct RISC-mediated cleavage, in some cases translational inhibition and DNA methylation can be the mode of action of miRNA-mediated gene silencing [19,20,21]
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