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Open Access Highly Accessed Research article

Construction of small RNA-mediated gene regulatory networks in the roots of rice (Oryza sativa)

Xiaoxia Ma1, Chaogang Shao2*, Huizhong Wang1, Yongfeng Jin3 and Yijun Meng1*

Author affiliations

1 College of Life and Environmental Sciences, Hangzhou Normal University, Xuelin Street 16#, Xiasha, Hangzhou 310036, P. R. China

2 College of Life Sciences, Huzhou Teachers College, Xueshi Road 1#, Huzhou 313000, P. R. China

3 Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China

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Citation and License

BMC Genomics 2013, 14:510  doi:10.1186/1471-2164-14-510

Published: 27 July 2013

Abstract

Background

The root systems play essential roles for plants to anchorage to the soil, and to exploit the mineral and water resources. The molecular mechanisms underlying root development have been extensively studied to improve root system architecture, especially for the crops. Several microRNA (miRNA) families have been demonstrated to be involved in plant root development. However, whether the other small RNA (sRNA) species, which occupy a dominant portion of the plant endogenous sRNA population, possess potential roles in root development remains unclear.

Results

In this study, by using sRNA high-throughput sequencing data, we made a comparison of the sRNA accumulation levels between the rice root tips and the whole roots. The sRNAs highly accumulated in the root tips and in the whole roots were extracted respectively. After Argonaute 1 (AGO1) enrichment analysis, the sRNAs with great potential of performing target cleavages were included for target prediction and degradome sequencing data-based validation. As a result, lists of the targets regulated by the AGO1-enriched sRNAs were obtained for both the root tips and the whole roots. Further evidences were identified from microarray data of the target genes to support some of the sRNA—target interactions. Specifically, the expression patterns of certain target genes in the root tips and the whole roots were contrary to those of the regulating sRNAs. Besides, several targets were indicated to play important roles in root development based on literature mining.

Conclusions

Taken together, the regulatory networks mediated by the sRNAs highly accumulated in the root tips or in the whole roots could advance our current understanding of the sRNA-involved molecular mechanisms underlying rice root development. And, the sRNA—target lists could serve as the basis for further functional investigations.

Keywords:
Small RNA; Whole root; Root tip; Argonaute 1; Degradome; Network; Rice (Oryza sativa)