Identification and characterization of hub genes underlying salt stress tolerance in rice (Oryza sativa L.)

Salt-tolerant genes (STGs) play a crucial role in protecting rice against salt-induced stress. Hub genes (HGs), which are connected to other genes in the gene network, have also been found to encode regulators of biological processes that remained elusive in rice salt stress tolerance. To confront the issue of salt stress tolerance, 348 differentially expressed STGs were selected responsive to salt tolerance in rice from a data search. Several CytoHubba algorithms were applied to sort out the HGs and detected 10 genes for comparative phylogenetic analysis, conserved motif detection, and gene structure determination. We detected and characterized 10 candidate HGs in the rice salt-stress network, including the ubiquitin gene, calcineurin B-like protein-interacting protein kinases genes, high-affinity potassium transporters genes, protein kinase domain gene, ATP-binding cassette subfamily gene, and phosphoenolpyruvate carboxylase gene. To understand the functional roles of these HGs, we critically analyzed the phylogenetic relationship, gene structure, domain architecture, conserved motifs, protein structure, and protein network through bioinformatics approaches. Moreover, gene ontology (GO) enrichment analysis stated that these HGs are involved in rice response to salt stress, K+ transmembrane transporter activity, protein phosphorylation, ion transport, and signal transduction. RNA-Seq analysis suggests that these salt-induced STGs might contribute to rice salt stress responses. Tissue-specific expression analysis indicated that these HGs might have various functions under salt stress. These outcomes of this study provide potential candidates for further in-depth functional studies in rice and their usefulness in salt-tolerant rice breeding programs.