Abstract

BackgroundMany plant species have been investigated in the last years for the identification and characterization of the corresponding miRNAs, nevertheless extensive studies are not yet available on barley (at the time of this writing). To extend and to update information on miRNAs and their targets in barley and to identify candidate polymorphisms at miRNA target sites, the features of previously known plant miRNAs have been used to systematically search for barley miRNA homologues and targets in the publicly available ESTs database. Matching sequences have then been related to Unigene clusters on which most of this study was based.ResultsOne hundred-fifty-six microRNA mature sequences belonging to 50 miRNA families have been found to significantly match at least one EST sequence in barley. As expected on the basis of phylogenetic relations, miRNAs putatively orthologous to those of Triticum are significantly over-represented inside the set of identified barley microRNA mature sequences. Many previously known and several putatively new miRNA/target pairs have been identified. When the predicted microRNA targets were grouped into functional categories, biological processes previously known to be regulated by miRNAs, such as development and response to biotic and abiotic stress, have been highlighted and most of the target molecular functions were related to transcription regulation. Candidate microRNA coding genes have been reported and genetic variation (SNPs/indels) both in functional regions of putative miRNAs (mature sequence) and at miRNA target sites has been found.ConclusionsThis study has provided an update of the information on barley miRNAs and their targets representing a foundation for future studies. Many of previously known plant microRNAs have homologues in barley with expected important roles during development, nutrient deprivation, biotic and abiotic stress response and other important physiological processes. Putative polymorphisms at miRNA target sites have been identified and they can represent an interesting source for the identification of functional genetic variability.

Highlights

  • Many plant species have been investigated in the last years for the identification and characterization of the corresponding miRNAs, extensive studies are not yet available on barley

  • Barley miRNAs Since only mature miRNA sequences rather than precursor sequences are conserved among plant species, mature miRNA sequences have been used as queries for BLAST search against Hordeum vulgare ESTs [10]

  • One hundred-fifty-six microRNA mature sequences belonging to 50 miRNA families have been found to significantly match at least one EST sequence in barley and could be related both to target or miRNA sequences, even if the probability is lower for the latter

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Summary

Introduction

Many plant species have been investigated in the last years for the identification and characterization of the corresponding miRNAs, extensive studies are not yet available on barley (at the time of this writing). MiRNAs act on gene regulation at post-transcriptional level, a phenomenon known in plants as PTGS (Post Transcriptional Gene Silencing), through sequence-based interaction with target mRNAs. Many plant species have been investigated during recent years for miRNAs identification and characterization. The current information available on barley refers to two papers [2,3]. Search based on evolutionary conservation has allowed the identification of miRNA families in many plant species, including those where the complete genome sequence is not available, as it is currently the case of barley. Without genome sequence information a powerful alternative data source comes from ESTs (Expressed Sequence Tags): currently 501,616 ESTs are available in barley http://www.ncbi.nlm.nih.gov/ dbEST/dbEST_summary.html [5]

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