Small RNA deep sequencing reveals the important role of micro RNA s in the halophyte Halostachys caspica

Summary Micro RNA s (mi RNA s), an extensive class of small regulatory RNA s, play versatile roles in plant growth and development as well as stress responses. However, the regulatory mechanism is unclear on mi RNA ‐mediated response to abiotic stress in plants. Halostachys caspica is a halophytic plant species and a great model for investigating plant response to salinity stress. However, no research has been performed on mi RNA s in H. caspica . In this study, we employed deep sequencing to identify both conserved and novel mi RNA s from salinity‐exposed H. caspica and its untreated control. Among the 13–19 million sequences generated from both treatments, a total of 170 conserved mi RNA s, belonging to 151 mi RNA families, were identified; among these mi RNA s, 31 were significantly up‐regulated and 48 were significantly down‐regulated by salinity stress. We also identified 102 novel mi RNA s from H. caspica ; among them, 12 mi RNA s were significantly up‐regulated and 13 were significantly down‐regulated by salinity. qRT ‐ PCR expression analysis validated the deep sequencing results and also demonstrated that mi RNA s and their targeted genes were responsive to high salt stress and existed a negative expression correlation between mi RNA s and their targets. mi RNA ‐target prediction, GO and KEGG analysis showed that mi RNA s were involved in salt stress‐related biological pathway, including calcium signalling pathway, MAPK signalling pathway, plant hormone signal transduction and flavonoid biosynthesis, etc. This suggests that mi RNA s play an important role in plant salt stress tolerance in H. caspica . This result could be used to improve salt tolerance in crops and woods.