Response of miRNAs and their targets to salt and drought stresses in cotton (Gossypium hirsutum L.)

• Certain miRNAs respond to salinity and drought stresses
• miRNA-mediated gene target also respond to abiotic stress.
• Certain miRNAs show perfect regulation relationship with their target gene.

MicroRNAs (miRNAs) are an important gene regulator, controlling almost all biological and metabolic processes, in both plants and animals. In this study, we investigated the effect of drought and salinity stress on the expression of miRNAs and their targets in cotton (Gossypium hirsutum L.). Our results show that the expression change of miRNAs and their targets were dose-dependent and tissue-dependent under salinity and drought conditions. The expression of miRNAs in leaf was down-regulated under higher salinity stress while shows variable patterns in other conditions. The highest fold-changes of miRNAs were miR398 in roots with 28.9 fold down-regulation under 0.25% NaCl treatment and miR395 in leaves with 7.6 fold down-regulation under 1% PEG treatment. The highest up-regulation of miRNA targets was AST in roots with 4.7 fold-change under 2.5% PEG and the gene with highest down-regulation was CUC1 in leaves with 25.6 fold-change under 0.25% NaCl treatment. Among seven miRNA-target pairs we studied, five pairs, miR156–SPL2, miR162–DCL1, miR159–TCP3, miR395–APS1 and miR396–GRF1, show significant regulation relationship in roots and leaves under salinity stress concentration.