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Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.)

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Abstract

Objectives

To identify drought stress-responsive conserved microRNA (miRNA) from Dongxiang wild rice (Oryza rufipogon Griff., DXWR) on a genome-wide scale, high-throughput sequencing technology was used to sequence libraries of DXWR samples, treated with and without drought stress.

Results

505 conserved miRNAs corresponding to 215 families were identified. 17 were significantly down-regulated and 16 were up-regulated under drought stress. Stem-loop qRT-PCR revealed the same expression patterns as high-throughput sequencing, suggesting the accuracy of the sequencing result was high. Potential target genes of the drought-responsive miRNA were predicted to be involved in diverse biological processes. Furthermore, 16 miRNA families were first identified to be involved in drought stress response from plants.

Conclusion

These results present a comprehensive view of the conserved miRNA and their expression patterns under drought stress for DXWR, which will provide valuable information and sequence resources for future basis studies.

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Acknowledgments

We thank Dr. Shannon R M Pinson (USDA-ARS Dale Bumpers National Rice Research Center, USA) for her advice and revision during preparation of the manuscript. This research was partially supported by the National Natural Science Foundation of China (31201191 and 31360327), the Natural Science Foundation of Jiangxi Province, China (20132BAB214009 and 20142BAB204012) and the Foundation of Jiangxi Educational Committee (GJJ14248).

Supporting information

Supplementary Table 1—Sequences of primers used for stem-loop qRT-PCR

Supplementary Table 2—Distribution of small RNA among 11 different categories for the control and drought stress-treatment libraries

Supplementary Table 3—Conserved miRNA identified by high-throughput sequencing in the control (DY_N) and drought stress-treatment (DY_D) libraries

Supplementary Table 4—The target genes of the drought stress-responsive miRNA

Author information

Authors and Affiliations

  1. College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China

    Fantao Zhang, Xiangdong Luo, Yi Zhou & Jiankun Xie

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  1. Fantao Zhang
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  2. Xiangdong Luo
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Correspondence to Jiankun Xie.

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Zhang, F., Luo, X., Zhou, Y. et al. Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.). Biotechnol Lett 38, 711–721 (2016). https://doi.org/10.1007/s10529-015-2012-0

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