Expression profile of miRNAs in Populus cathayana L. and Salix matsudana Koidz under salt stress

State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing 100091, China.
Molecular Biology Reports (Impact Factor: 2.02). 06/2012; 39(9):8645-54. DOI: 10.1007/s11033-012-1719-4
Source: PubMed


Soil salinization can lead to environmental and ecological problems worldwide. Abiotic stressors, including salinity, are suspected to regulate microRNA (miRNA) expression. Plants exposed to such abiotic stressors express specific miRNAs, which are genes encoding small non-coding RNAs of 20-24 nucleotides. miRNAs are known to exist widely in plant genomes, and are endogenous. A previous study used miRNA microarray technology and poly(A) polymerase-mediated qRT-PCR technology to analyze the expression profile of miRNAs in two types of plants, Populus cathayana L. (salt-sensitive plants) and Salix matsudana Koidz (highly salinity-tolerant plants), both belonging to the Salicaceae family. miRNA microarray hybridization revealed changes in expression of 161 miRNAs P. cathayana and 32 miRNAs in S. matsudana under salt stress. Differences in expression indicate that the same miRNA has different expression patterns in salt-sensitive plants and salt-tolerant plants under salt stress. These indicate that changes in expression of miRNAs might function as a response to varying salt concentrations. To examine this, we used qRT-PCR to select five miRNA family target genes involved in plant responses to salt stress. Upon saline treatment, the expressions of both ptc-miR474c and ptc-miR398b in P. cathayana were down-regulated, but were up-regulated in S. matsudana. Expression of the miR396 family in both types of plants was suppressed. Furthermore, we have analyzed the different expression patterns between P. cathayana and S. matsudana. Findings of this study can be utilized in future investigations of post-transcriptional gene regulation in P. cathayana and S. matsudana under saline stress.

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Available from: Zhuo Renying, Dec 20, 2013
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    • "miR396 was shown to be involved in temperature, salinity, cold, alkali and drought stress responses (Gao et al. 2010; Giacomelli et al. 2012; Kantar et al. 2011; Liu et al. 2009; Zhou et al. 2010, 2012), while miR166 was evidenced to play part in drought (Kantar et al. 2010, 2011). Biotic stress relevance of miR166 and miR396 was also reported repeatedly (Bazin et al. 2013; Hewezi et al. 2008, 2012; Zhou et al. 2012). In this study, with qRT-PCR, these miRNAs, predicted with high confidence from the LCG assembly , were comparatively quantified in leaf tissue of wheat, miR396 being the most abundant (Figs. 4 and 5). "
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    ABSTRACT: MicroRNAs are post-transcriptional regulators of gene expression, taking roles in a variety of fundamental biological processes. Hence, their identification, annotation and characterization are of great significance, especially in bread wheat, one of the main food sources for humans. The recent availability of 5× coverage Triticum aestivum L. whole-genome sequence provided us with the opportunity to perform a systematic prediction of a complete catalogue of wheat microRNAs. Using an in silico homology-based approach, stem-loop coding regions were derived from two assemblies, constructed from wheat 454 reads. To avoid the presence of pseudo-microRNAs in the final data set, transposable element related stem-loops were eliminated by repeat analysis. Overall, 52 putative wheat microRNAs were predicted, including seven, which have not been previously published. Moreover, with distinct analysis of the two different assemblies, both variety and representation of putative microRNA-coding stem-loops were found to be predominant in the intergenic regions. By searching available expressed sequences and small RNA library databases, expression evidence for 39 (out of 52) putative wheat microRNAs was provided. Expression of three of the predicted microRNAs (miR166, miR396 and miR528) was also comparatively quantified with real-time quantitative reverse transcription PCR. This is the first report on in silico prediction of a whole repertoire of bread wheat microRNAs, supported by the wet-lab validation.
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    Biochimie 11/2012; 95(4). DOI:10.1016/j.biochi.2012.10.025 · 2.96 Impact Factor
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    ABSTRACT: Background Populus euphratica is a representative model woody plant species for studying resistance to abiotic stresses such as drought and salt. Salt stress is one of the most common environmental factors that affect plant growth and development. MicroRNAs (miRNAs) are small, noncoding RNAs that have important regulatory functions in plant growth, development, and response to abiotic stress. Results To investigate the miRNAs involved in the salt-stress response, we constructed four small cDNA libraries from P. euphratica plantlets treated with or without salt (300 mM NaCl, 3 days) in either the root or leaf. Using high-throughput sequencing to identify miRNAs, we found 164 conserved miRNAs belonging to 44 families. Of these, 136 novel miRNAs were from the leaf, and 128 novel miRNAs were from the root. In response to salt stress, 95 miRNAs belonging to 46 conserved miRNAs families changed significantly, with 56 miRNAs upregulated and 39 miRNAs downregulated in the leaf. A comparison of the leaf and root tissues revealed 155 miRNAs belonging to 63 families with significantly altered expression, including 84 upregulated and 71 downregulated miRNAs. Furthermore, 479 target genes in the root and 541 targets of novel miRNAs in the leaf were predicted, and functional information was annotated using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Conclusions This study provides a novel visual field for understanding the regulatory roles of miRNAs in response to salt stress in Populus.
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