Genome-wide in silico identification and characterization of sodium-proton (Na+/H+) antiporters in Indica rice

Plant sodium/hydrogen (Na+/H+) antiporters (NHXs) are key Na+ transporters, and play vital roles in plant growth, development and abiotic stress responses, in particular salinity stress. Present study was aimed at genome-wide identification, comprehensive in silico characterization and involvement of NHX antiporters in plant development and abiotic stress responses of Indica rice (Oryza sativa subsp. indica). Though there are reports of screening of NHXs from Japonica rice, such reports are lacking from the Indica counterparts. In the current investigation, genome-wide screening of O. sativa Indica subspecies revealed sixteen NHX orthologous, and these were confirmed to be Na+/H+ exchangers. The identified OsNHXs were distributed across nine chromosomes of O. sativa Indica. Probable sites of the OsNHXs were cell membranes or vacuoles, as suggested by their sub-cellular localization. The cis-regulatory elements of OsNHX promoters indicated their involvement in environmental stress responses. OsNHXs were predicted to be targets of 91 miRNA candidates belonging to 10 families. Three-dimensional OsNHX protein structures were also predicted using bioinformatics tools. In order to gain insights into the functional roles of the identified OsNHXs, digital gene expression analysis was carried out and the results revealed that the expression levels of OsNHXs varied amongst the growth and developmental phases and under salinity and drought stress conditions. These results hold significance in identifying potent NHX candidates from Indica rice, having key roles in Na+ transport and in maintaining cellular ionic homeostasis, and can be further explored as potent candidate genes for engineering salinity tolerance in rice and other crop plants.