Identification of drought-responsive hub genes and their related miRNAs in Arabidopsis thaliana

Abstract Drought is important environmental stress that reduces the yield and quality of crops all around the world. The drought-responsive regulatory network is very complex in plants. MicroRNAs are an important gene expression regulator under drought conditions. Identifying drought-responsive genes and their related miRNAs helps us to provide valuable information on plant stress regulation by miRNAs in stress conditions. In this study, a microarray dataset of drought stress and well-water samples of Arabidopsis were analyzed to identify the common root and shoot genes in drought. GEO2R tool was used for identifying differentially expressed genes. Gene ontology enrichment, protein-protein interaction, pathway analysis, and potential miRNAs for hub genes were performed using bioinformatics tools. There were 486 and 288 DEGs of root and shoot tissue respectively. Venn diagram analysis demonstrated that 59 DEGs were common in both root and shoot tissues, including 51 upregulated genes and 8 downregulated genes enriched in response to water deprivation, response to osmotic stress, response to abscisic acid, response to oxidative stress, response to salt stress and other related pathways. Gene ontology and protein network analysis showed that TSPO, LTI78, AFP1, RAB18, LTI65, HAI1, HAI2, LEA4-5, LEA7, and F16B3.11 genes are hub genes in drought conditions. All hub genes except LEA7 and F16B3.11 were target genes of miRNAs. It seems that these genes and their related miRNAs can play a crucial role in drought response adaptation and they can be considered in breeding programs and genetic engineering for the production of drought-tolerant plants.