Identification and comparative analysis of differentially expressed miRNAs in leaves of two wheat (Triticum aestivum L.) genotypes during dehydration stress

Abstract

BackgroundMicroRNAs (miRNAs) play critical roles in the processes of plant growth and development, but little is known of their functions during dehydration stress in wheat. Moreover, the mechanisms by which miRNAs confer different levels of dehydration stress tolerance in different wheat genotypes are unclear.ResultsWe examined miRNA expressions in two different wheat genotypes, Hanxuan10, which is drought-tolerant, and Zhengyin1, which is drought-susceptible. Using a deep-sequencing method, we identified 367 differentially expressed miRNAs (including 46 conserved miRNAs and 321 novel miRNAs) and compared their expression levels in the two genotypes. Among them, 233 miRNAs were upregulated and 10 were downregulated in both wheat genotypes after dehydration stress. Interestingly, 13 miRNAs exhibited opposite patterns of expression in the two wheat genotypes, downregulation in the drought-tolerant cultivar and upregulation in the drought-susceptible cultivar. We also identified 111 miRNAs that were expressed predominantly in only one or the other genotype after dehydration stress. We verified the expression patterns of a number of representative miRNAs using qPCR analysis and northern blot, which produced results consistent with those of the deep-sequencing method. Moreover, monitoring the expression levels of 10 target genes by qPCR analysis revealed negative correlations with the levels of their corresponding miRNAs.ConclusionsThese results indicate that differentially expressed patterns of miRNAs between these two genotypes may play important roles in dehydration stress tolerance in wheat and may be a key factor in determining the levels of stress tolerance in different wheat genotypes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0413-9) contains supplementary material, which is available to authorized users.

Characterization of drought- and heat-responsive microRNAs in switchgrass

“…Sequencing profiles revealed that most miRNA families responded similarly to both the stressors (drought or heat) while a fewmiRNA families showed stress-specific response, i.e., induced or repressed only under drought or heat in switchgrass ( Table 2). The altered expression of several miRNAs following drought or heat in this study was largely in agreement with several earlier reports that studied miRNA responses to stress conditions ingrasses[40,41, [53][54][55][56][57][58][59][60][61][62][63][64][65][66].Nevertheless, there are alsoinstances in which our study did not correspond with some of the earlier reports. For instance,drought stress repressed the expression of miR166 in wheat [53], rice [57] and sugarcane [63] while we found it is induced in switchgrass.Drought downregulated the expression of miR167 and miR168 in switchgrass [40] andmiR168 in rice [57]butthese miRNAs are found to be up-regulated by drought in this study.The miR396 levels were repressed in wheat [53],rice [57] and sugarcane [63]under drought but it is up regulated under drought in the present study.…”

Abiotic stress miRNomes in the Triticeae

“…miR169 from barley was detected as upregulated in leaves while it is downregulated in roots. Another miRNA, miR159, showed induced expression in the leaves of wheat while it was downregulated in the roots (Gupta et al 2014; Ma et al 2015). Altered expression patterns of some miRNA families may directly be associated with the target specification of miRNAs since miRNAs can show multiple target preferences with respect to tissue type (Hackenberg et al 2014).…”

“…Interestingly, some miRNA families, for example miR159, miR167, and miR169, were detected as responsive to multiple stresses (Budak et al 2014; Sinha et al 2015; Budak et al 2015c). Alternatively, some miRNAs such as miR1432 and miR1137 displayed stress-specific expression patterns in several members of the Triticeae (Kantar et al 2010; Kantar et al 2011a; Gupta et al 2014; Ma et al 2015). Here, we aim to present a detailed overview of miRNA-based abiotic stress regulation in the Triticeae by critically reviewing the research on this topic.…”

Identification of Circular RNAs and Their Targets in Leaves of Triticum aestivum L. under Dehydration Stress

“…Along with the development of high-throughput sequencing technology and high-efficiency big data analysis, many more non-protein-coding genes are identified and characterized with response to environmental stress in plants. Previous studies have shown that non-protein-coding genes play vital roles in the stress response of wheat plant, including fungi-responsive long non-coding RNAs (lncRNAs) (Zhang et al, 2016) and dehydration responsive microRNAs (miRNAs) (Ma et al, 2015). The non-coding RNA itself, or interacting with other effectors as complex, is involved into the biochemical response directly or indirectly, regulating the expression of responsive functional genes at the transcriptional and/or translational levels (Zhang, 2015; Khaldun et al, 2016).…”