ArticleBMC genomics2015
An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 33 citations in OpenAlex.
- Application of Artificial Intelligence Technology in Plant MicroRNA Research: Progress, Challenges, and Prospects.International journal of molecular sciences · 2025Review
- Polyploidization: A Biological Force That Enhances Stress Resistance.International journal of molecular sciences · 2024Review
- Genome-Wide Identification and Functional Characterization of Auxin Response Factor (ARF) Genes in Eggplant.International journal of molecular sciences · 2022Article
- Computational screening of miRNAs and their targets in saffron (Crocus sativus L.) by transcriptome mining.Planta · 2021Article
- Integrated Metabolomic and Transcriptomic Analysis of the Flavonoid Accumulation in the Leaves ofFrontiers in plant science · 2021Article
- Identification, evolution, expression, and docking studies of fatty acid desaturase genes in wheat (Triticum aestivum L.).BMC genomics · 2020Article
- The adaptation strategies of Herpetospermum pedunculosum (Ser.) Baill at altitude gradient of the Tibetan plateau by physiological and metabolomic methods.BMC genomics · 2019Article
- Development of species specific putative miRNA and its target prediction tool in wheat (Triticum aestivum L.).Scientific reports · 2019Article
- miPIE: NGS-based Prediction of miRNA Using Integrated Evidence.Scientific reports · 2019Article
- Identification and characterization of durum wheat microRNAs in leaf and root tissues.Functional & integrative genomics · 2017Article
- Water-deficit stress-responsive microRNAs and their targets in four durum wheat genotypes.Functional & integrative genomics · 2017Article
- Long noncoding miRNA gene represses wheat β-diketone waxes.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Genome-Wide Identification of MicroRNAs in Leaves and the Developing Head of Four Durum Genotypes during Water Deficit Stress.PloS one · 2015Article
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWheat 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.
resultsWe 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.
conclusionThis 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.
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