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Cloning and characterization of microRNAs from wheat (Triticum aestivum L.)

Yingyin Yao12, Ganggang Guo12, Zhongfu Ni12, Ramanjulu Sunkar3, Jinkun Du12, Jian-Kang Zhu4 and Qixin Sun12*

Author Affiliations

1 Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China

2 National Plant Gene Research Centre (Beijing), Beijing 100094, China

3 Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK74078, USA

4 Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA

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Genome Biology 2007, 8:R96  doi:10.1186/gb-2007-8-6-r96

Published: 1 June 2007

Abstract

Background

MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited to a few model plant species, such as Arabidopsis, rice and Populus, whose genomes have been sequenced. Wheat is one of the most important cereal crops worldwide. To date, only a few conserved miRNAs have been predicted in wheat and the computational identification of wheat miRNAs requires the genome sequence, which is unknown.

Results

To identify novel as well as conserved miRNAs in wheat (Triticum aestivum L.), we constructed a small RNA library. High throughput sequencing of the library and subsequent analysis revealed the identification of 58 miRNAs, comprising 43 miRNA families. Of these, 35 miRNAs belong to 20 conserved miRNA families. The remaining 23 miRNAs are novel and form 23 miRNA families in wheat; more importantly, 4 of these new miRNAs (miR506, miR510, miR514 and miR516) appear to be monocot-specific. Northern blot analysis indicated that some of the new miRNAs are preferentially expressed in certain tissues. Based on sequence homology, we predicted 46 potential targets. Thus, we have identified a large number of monocot-specific and wheat-specific miRNAs. These results indicate that both conserved and wheat-specific miRNAs play important roles in wheat growth and development, stress responses and other physiological processes.

Conclusion

This study led to the discovery of 58 wheat miRNAs comprising 43 miRNA families; 20 of these families are conserved and 23 are novel in wheat. It provides a first large scale cloning and characterization of wheat miRNAs and their predicted targets.