Identification of salt-stress responsive microRNAs from Solanum lycopersicum and Solanum pimpinellifolium

MicroRNAs (miRNAs) are endogenous noncoding small RNAs, which play versatile roles in plant growth and development as well as stress response. Soil salinity is a major environmental limit for crop production. To identify conserved and novel miRNAs in Solanum lycopersicum and Solanum pimpinellifolium, and to characterize miRNAs that could play a role in salt tolerance, we have generated miRNA libraries from NaCl-treated and untreated seedlings of two genotypes from the above species. A total of 95 conserved miRNAs, belonging to 45 families, and 254 novel ones were detected. Among these miRNAs, 14 conserved and 109 novel miRNAs showed significant changes in expression under salt stress. After target gene prediction, gene ontology and pathway analysis of the target genes showed that miRNAs were involved in salt-stress related biological pathways, including photosynthesis, plant hormone signal transduction, oxidative phosphorylation, phosphatidylinositol signaling system, and calcium ion homeostasis. And sly-miR156e-5p, slymiRn23b, sly-miRn50a and some other miRNAs were involved in the salt stress response of S. pimpinellifolium. Our results suggested that miRNAs play essential roles in the salt tolerance of tomato.