Salinity is an increasingly important agricultural problem. The metabolism of plants are affected by salt stress and in recent years many studies have been devoted to understanding the molecular mechanisms of plant salt tolerance. Sugarcane cultivars differ in their responses to salt stress. There are several miRNAs that have been identified in different species, but only a few studies have been performed to analyze their expression in response to salt stress in sugarcane.
In the present study, the results indicated miR160, miR164, miR172, miR390, miR393, miR408, miR529, miR827, miR1432, have been implicated in stress caused by salt [15, 17]. Analysis of the relative expression of all these miRNAs (Fig. 1) showed that miR160 had the highest expression in NaCl treatment. Others showed small differences in expression compared with the control. The result shown that there are significant differences in expression of miRNAs and their targets. However, some miRNAs had significant expression. Low expression of miRNAs showed significant difference profiles depending on the cultivar .
miR390 targeting ARF transcription factors  has been found with different expression in sugarcane. ARF is one of the targeted TFs which involved in rooting, responder to drought and salinity stress, plant develops, response to auxin and auxin signaling . This microRNA is preparing the background for Aux/IAA protein degradation by regulating the activity of SCF E3 Ubiquitin ligase. In current study the expression of miR160 is extremely decrease while the expression of ARF gene is increase. The possible reason for this expression pattern is providing an appropriate condition for keep on the growth of plants under salinity stress. This expression pattern show increasing in the length of lateral roots which make absorption of water more easily in these limitation conditions.
In sugarcane, NAC TFs and ARFs TFs have been validated as targets of miR164, miR160, respectively . NAC TF family involved in response to abiotic stresses such as salinity and drought stresses . The increasing in NAC expression can make plants to be tolerant to abiotic stresses like salinity and drought. The studies have shown that this TF can directly bind to promoter of genes are involved in salinity and drought stress and induce their expression . The recent studies have proofed the interaction between this TF and miR164. This TF is part of plants signal transduction which can induce many physiological mechanisms under salinity stress. Under salinity stress the expression of miR164 is decrease while the expression of NAC is increased. This expression pattern has represented the effect of plant signaling network and ionic adjustment of homeostasis and finally stabilize of plant growth under salinity stress .
miR172 targeting AP2-like ethylene-responsive transcription factors  have been found with different expression in sugarcane. TFAP is involved in many cellular aspects such as controlling growth factor, development and apoptosis . Key approaches to response abiotic stress, such as salinity is decrease growth and development and activate the apoptosis mechanism. In this study the expression of miR172 is decreased and the expression of TFAP is increased. This expression pattern is happening in order to limit the growth and development and the activate apoptosis mechanism. Phosphorylation is a mechanism which is phosphate can be added or remove by protein kinases and activate functional proteins .
Protein kinase genes (PLPRKs) are potential targets for miR390. Previous studies have shown that the expression of miR390 is decreased under salinity stress and its target has increased in expression . In this study as previous studies the expression of miR390 decrease whiles the expression of PLPRK increase. This cause activation many protein kinases and proteins that is involved in salinity stress.
In plants there is many proteins cause sensitivity under certain conditions like abiotic stress. Tolerant plants have mechanisms that inducing degradation of these kind of proteins. EBF gene is one of the genes that involves in proteins degradations. This gene is potentially target of miR393 .
In this study the expression of miR393 strongly induced by NaCl treatment, while EB-Fbox gene has increased in expression under this stress. It can say that this increasing in EB-Fbox is for degrading the proteins that cause sensitivity in sugarcane cultivars under salinity stress.
Many of studies generally have shown that under salinity stress, absorb of micro element, such as Copper ion in plants is increased. Since the presence of Copper ion is poisonous for the plants cell, this ion is extremely controlled by molecular mechanisms. BBP gene (Basic Blue Protein) is part of this molecular mechanism that involved in Copper ion control. This gene has an important enzymatic role that especially controls the level of Copper ion under salinity stress. On other hand, when plants are under abiotic stress like salinity stress, the oxidative stress is induced. In this condition, enzyme like superoxide dismutase is active and control the oxidative stress. The activation of SOD enzyme is regulated by BBP gene .
miR408 targets the mRNAs of the BBP gene and Laccase (LAC). The results had shown that expression of miR408 under salinity stress is decreased and the expression of BBP gene is increased. Squamosa Binding Protein (SBP) has roles in plant leaf development, vegetative to reproductive phase transition, fruit development and gibberellin signal transduction. When plants are encounter a harsh environment such as abiotic stress in their life cycle, they are accelerating the development of leaves and vegetative to reproductive transition. This event is controlled by molecular mechanisms and changing in genes expression like SBP gene. The expression of SBP gene is regulated by miR529 .
We also found opposite expression patterns of these three miRNAs (miR529, 827 and 1432) and their target gene (SPL9, SDP and CBP).
Under salinity stress, nutrition of plants is disrupted and causing extreme damage to plant growth. The phosphorus is very important for plant growth and salinity stress its absorption is disrupted. The plant has developed many physiological and molecular mechanisms to absorb P ion under salinity stress. One mechanism is activated SPX-domain containing protein (SDP) under this condition. This protein is involved in the adjustment of P homeostasis and plants by activating these proteins in salinity stress confront with P starvation . It has shown that this gene is regulated by miR827 in plants. The result of this study showed decreasing in miR827 expression and increasing SDP expression under salinity stress, which they match with previous studies in other plants.
Plants are sessile and when they confront with the stresses, they make changes within their cells and organelles. Identification of stresses and response to them is regulated many signal pathways. In this pathway there is many proteins are involved. One known protein that play role in signal transduction under stresses is CBP (Calcium Binding Protein). MiR1432 is targeting this protein in plants. Under stress the cytosol filled by Ca2+ and then CBP bind to Ca2+ and provides conditions to trigger many signal pathways involving in regulating and responding to stresses such as salinity stress . MiR1432 by decreasing its expression and increasing CBP expression, play its role in salinity response. In this study expression of miR1432 decrease and CBP expression is increased.