NDLI: An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress

Content Provider	Springer Nature : BioMed Central
Author	Agharbaoui, Zahra Leclercq, Mickael Remita, Mohamed Amine Badawi, Mohamed A Lord, Etienne Houde, Mario Danyluk, Jean Diallo, Abdoulaye Baniré Sarhan, Fathey
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. 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.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-015-1490-8.pdf
Ending Page	17
Page Count	17
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-015-1490-8
Journal	BMC Genomics
Issue Number	1
Volume Number	16
Language	English
Publisher	BioMed Central
Publisher Date	2015-04-24
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Triticum aestivum. L Abiotic stress Development Deep sequencing MiRNA prediction Expressed sequenced tags Vernalization
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress

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An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress

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An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress

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