Salt-responsive miRNA in root of Thellungiella salsuginea
Fei Gao, Jing Chen, Xin Sui, Yijun Zhou^*

College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
*Corresponding author：Tel: (+8610) 6893 2922; Fax: (+8610) 6893 6927; E-mail: queenzhou@263.net; zhouyijun@muc.edu.cn

Abstract
MicroRNA (miRNA) has been administrated as a key regulatory component in plant stress adaptation. Thellungiella salsuginea (halophila), a salt tolerant relative of Arabidopsis, is a good model used in plant salt tolerance studies, however, there is no report on identification and stress response profiling of miRNA in T. salsuginea. In the present study, Illumina sequencing generated two small RNA libraries using RNA isolated from high-salinity (SS) treated and untreated (CK) roots of T. salsuginea. Informatics analysis identified 49 conserved miRNA generated from 74 conserved miRNA precursors and 60 novel miRNA generated from 79 precursors, respectively. Comparing the reads of miRNA in CK and SS libraries identified 18 salt-responsive (change ratio > 1.5) conserved miRNA including 13 up-regulated (including miR160b, miR166-1, mir171c-1, miR2111a, mir319-2, mir394, and mir396) and 5 down-regulated (including miR167-1 miR395a, miR398a, and miR399b) conserved Thellungiella miRNAs. Twenty-nine salt-responsive including 6 up-regulated and 23 down-regulated novel Thellungiella miRNAs were also identified. Quantitative RT-PCRs were performed to validated these miRNA and expression profile. Target gene prediction and degradome sequencing revealed that these salt-responsive miRNA may participate in salt stress response in Thellungiella root by regulating the gene expression of transcription factors like ARF, GRF, TCP, SCL, NF-YC, cell cycle related protein like CYCLIN A and enzymes like CSD and ATP sulphurylase. Finally, a network model regulating the miRNA mediated salt stress response in Thellungiella root was proposed. Identification of miRNAs participating in stress response of T. salsuginea root will improve our understanding on molecular mechanisms of plant salt tolerance.

Key Words: Thellungiella salsuginea; root; salt stress; miRNA