title: An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biological Sciences, University of Quebec in Montreal, Montreal, Canada. agharbaoui.zahra@uqam.ca.
authors.forename: Zahra
authors.initials: Z
authors.lastname: Agharbaoui
authors.affiliation: Department of Computer Sciences, University of Quebec in Montreal, Montreal, Canada. mickael.leclercq@mail.mcgill.ca.|School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, QC, Canada. mickael.leclercq@mail.mcgill.ca.
authors.forename: Mickael
authors.initials: M
authors.lastname: Leclercq
authors.affiliation: Department of Computer Sciences, University of Quebec in Montreal, Montreal, Canada. remita.mohamed_amine@courrier.uqam.ca.
authors.forename: Mohamed Amine
authors.initials: MA
authors.lastname: Remita
authors.affiliation: Department of Biological Sciences, University of Quebec in Montreal, Montreal, Canada. badawi.mohamed@courrier.uqam.ca.
authors.forename: Mohamed A
authors.initials: MA
authors.lastname: Badawi
authors.affiliation: Department of Computer Sciences, University of Quebec in Montreal, Montreal, Canada. lord.etienne@courrier.uqam.ca.
authors.forename: Etienne
authors.initials: E
authors.lastname: Lord
authors.affiliation: Department of Biological Sciences, University of Quebec in Montreal, Montreal, Canada. houde.mario@uqam.ca.
authors.forename: Mario
authors.initials: M
authors.lastname: Houde
authors.affiliation: Department of Biological Sciences, University of Quebec in Montreal, Montreal, Canada. danyluk.jean@uqam.ca.
authors.forename: Jean
authors.initials: J
authors.lastname: Danyluk
authors.affiliation: Department of Computer Sciences, University of Quebec in Montreal, Montreal, Canada. diallo.abdoulaye@uqam.ca.
authors.forename: Abdoulaye Baniré
authors.initials: AB
authors.lastname: Diallo
authors.affiliation: Department of Biological Sciences, University of Quebec in Montreal, Montreal, Canada. sarhan.fathey@uqam.ca.
authors.forename: Fathey
authors.initials: F
authors.lastname: Sarhan
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D000069550:Machine Learning; D035683:MicroRNAs / Q000032:analysis*; D011123:Polyploidy; D018749:RNA, Plant / Q000032:analysis*; D013045:Species Specificity; D013312:Stress, Physiological; D014908:Triticum / Q000235:genetics* / Q000254:growth & development*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant