Response of microRNAs to cold treatment in the young spikes of common wheat

Abstract

BackgroundMicroRNAs (miRNAs) are a class of small non-coding RNAs that play important roles in biotic and abiotic stresses by regulating their target genes. For common wheat, spring frost damage frequently occurs, especially when low temperature coincides with plants at early floral organ differentiation, which may result in significant yield loss. Up to date, the role of miRNAs in wheat response to frost stress is not well understood.ResultsWe report here the sequencing of small RNA transcriptomes from the young spikes that were treated with cold stress and the comparative analysis with those of the control. A total of 192 conserved miRNAs from 105 families and nine novel miRNAs were identified. Among them, 34 conserved and five novel miRNAs were differentially expressed between the cold-stressed samples and the controls. The expression patterns of 18 miRNAs were further validated by quantitative real time polymerase chain reaction (qRT-PCR). Moreover, nearly half of the miRNAs were cross inducible by biotic and abiotic stresses when compared with previously published work. Target genes were predicted and validated by degradome sequencing. Gene Ontology (GO) enrichment analysis showed that the target genes of differentially expressed miRNAs were enriched for response to the stimulus, regulation of transcription, and ion transport functions. Since many targets of differentially expressed miRNAs were transcription factors that are associated with floral development such as ARF, SPB (Squamosa Promoter Binding like protein), MADS-box (MCM1, AG, DEFA and SRF), MYB, SPX (SYG1, Pho81 and XPR1), TCP (TEOSINTE BRANCHED, Cycloidea and PCF), and PPR (PentatricoPeptide Repeat) genes, cold-altered miRNA expression may cause abnormal reproductive organ development.ConclusionAnalysis of small RNA transcriptomes and their target genes provide new insight into miRNA regulation in developing wheat inflorescences under cold stress. MiRNAs provide another layer of gene regulation in cold stress response that can be genetically manipulated to reduce yield loss in wheat.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3556-2) contains supplementary material, which is available to authorized users.

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

“…Several studies indicate that auxin and microRNAs play essential roles in plant cold stress response [27,30,83]. Auxin plays a pivotal role in regulating temperature stress response, and high-temperature stress response directly affects the auxin biosynthesis through altering phytochrome interacting factors (PIFs) expression [84].…”

“…miRNAs bind to complementary mRNA molecules and act as negative regulators of gene expression through endonucleolytic cleavage or translational repression of the cognate mRNA targets [24]. Lately, miRNA regulation of stress response pathway has been established in several plant species [25][26][27][28]. Consistently, a large number of cold stress responsive microRNAs have been identi ed in various plant species with variable results in different reports [27,29,30].…”

Evolution of PHAS loci in the young spike of Allohexaploid wheat

“…To validate whether these PHAS transcripts can be indeed cleaved by miR2118 and miR2275, we downloaded the degradome sequences from the GEO datasets for the young spike tissue under cold stress by Song et al [29], which corresponds to the small RNA datasets of the AM stage of young spike (control samples, SRR3680677 and SRR3680678; and cold stress samples at 0°C after 48 h, SRR3680679 and SRR3690680). According to the abundance of reads along the whole transcripts, using the Cleaveland program [30] (P-value < 0.05 and the category <= 2), miR2118 and miR2275 were considered to be interacted between PHAS transcripts and miRNAs.…”

“…To understand whether the PHAS loci were regulated by miR2118 and miR2275 in wheat, we used the Targetfinder program [28] to predict the miRNA target sites in the PHAS sequences with scores less than four. To validate whether the miRNAs can indeed cleave the predicted targets, we downloaded the degradome (SRP076763) datasets from the GEO database, including the control and cold treatment datasets [29]. The degradome datasets with the control and cold stress samples corresponded to the small RNA datasets for the control (SRR3680677 and SRR3680678) and cold stress samples (SRR3680679 and SRR3690680).…”

Evolution of PHAS Loci in the Young Spike of Allohexaploid Wheat

“…The production of the PHAS loci could be initiated by miR2118 and miR2275, and then generate the To validate whether these PHAS transcripts can be indeed cleaved by miR2118 and miR2275, we downloaded the degradome sequences from the GEO datasets for the young spike tissue under cold stress by Song et al [29], which corresponds to the small RNA datasets of the AM stage of young spike (control samples, SRR3680677 and SRR3680678; and cold stress samples at 0°C after 48 hours, SRR3680679 and SRR3690680). According to the abundance of reads along the whole transcripts, using the Cleaveland program [30] (P-value < 0.05 and the category <= 2), miR2118 and miR2275 were considered to be interacted between PHAS transcripts and miRNAs.…”