An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress
| Autor: | Fathey Sarhan, Mario Houde, Abdoulaye Baniré Diallo, Etienne Lord, Jean Danyluk, Mohamed A. Badawi, Mohamed Amine Remita, Zahra Agharbaoui, Mickael Leclercq |
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| Rok vydání: | 2015 |
| Předmět: |
Deep sequencing
Biology Development Proteomics MiRBase Machine Learning Polyploidy Species Specificity Vernalization Gene Expression Regulation Plant Stress Physiological Genetics MiRNA prediction Triticum 2. Zero hunger Abiotic component Regulation of gene expression Expressed sequenced tags Abiotic stress Gene Expression Profiling Methodology Article food and beverages Computational Biology 15. Life on land Gene expression profiling MicroRNAs RNA Plant Triticum aestivum. L DNA microarray Biotechnology |
| Zdroj: | BMC Genomics |
| ISSN: | 1471-2164 |
| Popis: | Background Wheat is a major staple crop with broad adaptability to a wide range of environmental conditions. This adaptability involves several stress and developmentally responsive genes, in which microRNAs (miRNAs) have emerged as important regulatory factors. However, the currently used approaches to identify miRNAs in this polyploid complex system focus on conserved and highly expressed miRNAs avoiding regularly those that are often lineage-specific, condition-specific, or appeared recently in evolution. In addition, many environmental and biological factors affecting miRNA expression were not yet considered, resulting still in an incomplete repertoire of wheat miRNAs. Results We developed a conservation-independent technique based on an integrative approach that combines machine learning, bioinformatic tools, biological insights of known miRNA expression profiles and universal criteria of plant miRNAs to identify miRNAs with more confidence. The developed pipeline can potentially identify novel wheat miRNAs that share features common to several species or that are species specific or clade specific. It allowed the discovery of 199 miRNA candidates associated with different abiotic stresses and development stages. We also highlight from the raw data 267 miRNAs conserved with 43 miRBase families. The predicted miRNAs are highly associated with abiotic stress responses, tolerance and development. GO enrichment analysis showed that they may play biological and physiological roles associated with cold, salt and aluminum (Al) through auxin signaling pathways, regulation of gene expression, ubiquitination, transport, carbohydrates, gibberellins, lipid, glutathione and secondary metabolism, photosynthesis, as well as floral transition and flowering. Conclusion This approach provides a broad repertoire of hexaploid wheat miRNAs associated with abiotic stress responses, tolerance and development. These valuable resources of expressed wheat miRNAs will help in elucidating the regulatory mechanisms involved in freezing and Al responses and tolerance mechanisms as well as for development and flowering. In the long term, it may help in breeding stress tolerant plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1490-8) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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