<p>Abstract</p> <p>Background</p> <p>Rice (<it>Oryza sativa</it> L.), one of the most important food crop in the world, is considered to be a salt-sensitive crop. Excess levels of salt adversely affect all the major metabolic activities, including cell wall damage, cytoplasmic lysis and genomic stability. In order to cope with salt stress, plants have evolved high degrees of developmental plasticity, including adaptation via cascades of molecular networks and changes in gene expression profiles. Posttranscriptional regulation, through the activity of microRNAs, also plays an important role in the plant response to salinity conditions. MicroRNAs are small endogenous RNAs that modulate gene expression and are involved in the most essential physiological processes, including plant development and adaptation to environmental changes.</p> <p>Results</p> <p>In the present study, we investigated the expression profiles of osa-MIR414, osa-MIR408 and osa-MIR164e along with their targeted genes, under salinity stress conditions in wild type and transgenic rice plants ectopically expressing the <it>PDH45</it> (Pea DNA Helicase) gene. The present miRNAs were predicted to target the <it>OsABP</it> (ATP-Binding Protein), <it>OsDSHCT</it> (DOB1/SK12/helY-like DEAD-box Helicase) and <it>OsDBH</it> (DEAD-Box Helicase) genes, included in the DEAD-box helicase family. An <it>in silico</it> characterization of the proteins was performed and the miRNAs predicted targets were validated by RLM-5′RACE. The qRT-PCR analysis showed that the <it>OsABP</it>, <it>OsDBH</it> and <it>OsDSHCT</it> genes were up-regulated in response to 100 and 200 mM NaCl treatments. The present study also highlighted an increased accumulation of the gene transcripts in wild type plants, with the exception of the <it>OsABP</it> mRNA which showed the highest level (15.1-fold change compared to control) in the transgenic plants treated with 200 mM NaCl. Salinity treatments also affected the expression of osa-MIR414, osa-MIR164e and osa-MIR408, found to be significantly down-regulated, although the changes in miRNA expression were limited.</p> <p>Conclusions</p> <p>Osa-MIR414, osa-MIR164e and osa-MIR408 were experimentally validated for the first time in plants as targeting the <it>OsABP</it>, <it>OsDBH</it> and <it>OsDSHCT</it> genes. Our data showed that that the genes were up-regulated and the miRNAs were down-regulated in relation to salt stress. The negative correlation between the miRNAs and their targets was proven.</p
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