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Global identification of miRNAs and targets in Populus euphratica under salt stress

Plant Molecular Biology volume 81, pages 525–539 (2013)Cite this article

Abstract

Populus euphratica, a typical hydro-halophyte, is ideal for studying salt stress responses in woody plants. MicroRNAs (miRNAs) are endogenous non-coding small RNAs that fulfilled an important post-transcriptional regulatory function. MiRNA may regulate tolerance to salt stress but this has not been widely studied in P. euphratica. In this investigation, the small RNAome, degradome and transcriptome were studied in salt stress treated P. euphratica by deep sequencing. Two hundred and eleven conserved miRNAs between Populus trichocarpa and P. euphratica have been found. In addition, 162 new miRNAs, belonging to 93 families, were identified in P. euphratica. Degradome sequencing experimentally verified 112 targets that belonged to 51 identified miRNAs, few of which were known previously in P. euphratica. Transcriptome profiling showed that expression of 15 miRNA-target pairs displayed reverse changing pattern under salt stress. Together, these results indicate that, in P. euphratica under salt stress, a large number of new miRNAs could be discovered, and both known and new miRNA were functionally cleaving to their target mRNA. Expression of miRNA and target were correspondingly induced by salt stress but that it was a complex process in P. euphratica.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (30972339, 31070597, 30730077), the Ministry of Science and Technology of China (2009CB119101), the Scientific Research and Graduate Training Joint Programs from BMEC (Regulation of Tree WUE) and National Science Foundation (NSF) Plant Genome Program (DBI0922604). B.L. was supported by Peking-Yale Joint Center Monsanto Fellowship, a fellowship from the China Scholarship Council and Beijing Forestry University Technology Innovation Program (BLYJ200902).

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Affiliations

  1. College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, People’s Republic of China

    Bosheng Li, Hui Duan, Weilun Yin & Xinli Xia

  2. College of Forestry, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, People’s Republic of China

    Bosheng Li, Weilun Yin & Xinli Xia

  3. National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, People’s Republic of China

    Bosheng Li, Hui Duan, Weilun Yin & Xinli Xia

  4. Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA

    Bosheng Li, Jigang Li & Xing Wang Deng

  5. Beijing Forestry University, Mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing, People’s Republic of China

    Weilun Yin & Xinli Xia

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  1. Bosheng Li
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  2. Hui Duan
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  3. Jigang Li
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Correspondence to Weilun Yin or Xinli Xia.

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Li, B., Duan, H., Li, J. et al. Global identification of miRNAs and targets in Populus euphratica under salt stress. Plant Mol Biol 81, 525–539 (2013). https://doi.org/10.1007/s11103-013-0010-y

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  • DOI: https://doi.org/10.1007/s11103-013-0010-y

Keywords

  • Populus euphratica
  • Salt stress
  • Small RNAome
  • Degradome
  • Transcriptome