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Open Access Research article

Genome-wide identification of Thellungiella salsuginea microRNAs with putative roles in the salt stress response

Quan Zhang1, Chuanzhi Zhao2, Ming Li2, Wei Sun1, Yan Liu1, Han Xia2, Mingnan Sun2, Aiqin Li2, Changsheng Li2, Shuzhen Zhao2, Lei Hou2, Jean-François Picimbon2, Xingjun Wang12* and Yanxiu Zhao1*

Author Affiliations

1 College of Life Sciences, Shandong Normal University, Jinan 250014, PR China

2 Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, PR China

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BMC Plant Biology 2013, 13:180  doi:10.1186/1471-2229-13-180

Published: 15 November 2013

Abstract

Background

MicroRNAs are key regulators of plant growth and development with important roles in environmental adaptation. The microRNAs from the halophyte species Thellungiella salsuginea (salt cress), which exhibits extreme salt stress tolerance, remain to be investigated. The sequenced genome of T. salsuginea and the availability of high-throughput sequencing technology enabled us to discover the conserved and novel miRNAs in this plant species. It is interesting to identify the microRNAs from T. salsuginea genome wide and study their roles in salt stress response.

Results

In this study, two T. salsuginea small RNA libraries were constructed and sequenced using Solexa technology. We identified 109 miRNAs that had previously been reported in other plant species. A total of 137 novel miRNA candidates were identified, among which the miR* sequence of 26 miRNAs was detected. In addition, 143 and 425 target mRNAs were predicted for the previously identified and Thellungiella-specific miRNAs, respectively. A quarter of these putative targets encode transcription factors. Furthermore, numerous signaling factor encoding genes, defense-related genes, and transporter encoding genes were amongst the identified targets, some of which were shown to be important for salt tolerance. Cleavage sites of seven target genes were validated by 5’ RACE, and some of the miRNAs were confirmed by qRT-PCR analysis. The expression levels of 26 known miRNAs in the roots and leaves of plants subjected to NaCl treatment were determined by Affymetrix microarray analysis. The expression of most tested miRNA families was up- or down-regulated upon NaCl treatment. Differential response patterns between the leaves and roots were observed for these miRNAs.

Conclusions

Our results indicated that diverse set of miRNAs of T. salsuginea were responsive to salt stress and could play an important role in the salt stress response.

Keywords:
Thellungiella salsuginea; Salt stress; miRNA identification; Solexa sequencing; Expression analysis