MicroRNA Signatures of Drought Signaling in Rice Root.
BACKGROUND
Drought stress is one of the most important abiotic stresses and the main constraint to rice agriculture. MicroRNA-mediated post-transcriptional gene regulation is one of the ways to establish drought stress tolerance in plants. MiRNAs are 20-24-nt regulatory RNAs that play an important role in regulating plant gene expression upon exposure to biotic and abiotic stresses.


RESULTS
In this study, we applied a partial root drying system as well as a complete root drying system to identify miRNAs involved in conditions of drought stress, drought signaling and wet signaling using high-throughput sequencing. To this end, we produced four small RNA libraries: (1) fully-watered (WW), (2) fully-droughted (WD), and split-root systems where (3) one-half was well watered (SpWW) and (4) the other half was water-deprived (SpWD). Our analysis revealed 10,671 and 783 unique known and novel miRNA reads in all libraries, respectively. We identified, 65 (52 known + 13 novel), 72 (61 known + 11 novel) and 51 (38 known + 13 novel) miRNAs that showed differential expression under conditions of drought stress, drought signaling and wet signaling, respectively. The results of quantitative real-time PCR showed expression patterns similar to the high-throughput sequencing results. Furthermore, our target prediction led to the identification of 244, 341 and 239 unique target genes for drought-stress-, drought-signaling- and wet-signaling-responsive miRNAs, respectively.


CONCLUSIONS
Our results suggest that miRNAs that are responsive under different conditions could play different roles in the regulation of abscisic acid signaling, calcium signaling, detoxification and lateral root formation.
Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran.|Department of Plant Breeding, Science and Research Branch, Islamic Azad University, Tehran, Iran.
Behnam
B
Bakhshi
Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran.
Ehsan
E
Mohseni Fard
Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran.
Nava
N
Nikpay
Department of Biotechnology, Payame Noor University, Tehran, Iran.
Mohammad Ali
MA
Ebrahimi
Department of Agronomy and Plant Breeding, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
Mohammad Reza
MR
Bihamta
Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran.
Mohsen
M
Mardi
Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran.|Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
Ghasem Hosseini
GH
Salekdeh
D000222:Adaptation, Physiological; D035683:MicroRNAs / Q000378:metabolism*; D012275:Oryza / Q000378:metabolism*; D018517:Plant Roots / Q000378:metabolism*; D018520:Plant Shoots / Q000378:metabolism*; D018749:RNA, Plant / Q000378:metabolism*; D013312:Stress, Physiological / Q000502:physiology*
D035683:MicroRNAs; D018749:RNA, Plant