Integrative gene network analysis of rice transcriptome to identification of key microRNAs involved in salinity stress

Salt stress is a harsh abiotic stress that decreases the crop yield dramatically. Rice (Oryza sativa), a majorcereal, the main food source for many countries, is sensitive to this stress. Understanding the molecularmechanisms of rice under salt stress is a pivotal factor for developing stress-tolerant genotypes. Therefore,an integrative transcriptome data analysis was performed. For this purpose, some RNA-seq data wereretrieved from European Bioinformatics Institute (EBI) database. CLC Genomics Workbench v.۱۲ softwareused for data analysis. After quality control, reads were mapped to rice reference genome. The adjusted Pvalues(FDR < ۰.۰۱) were considered the significant and, thus, differentially expressed genes (DEGs) wereused for further analysis. Gene ontology analysis of DEGs showed that the genes were enriched for responseto cellular process, metabolic process, organic substance metabolic process in biological process category.Furthermore, the DEGs in molecular function category were enriched for catalytic activity, organic cycliccompound binding and oxidoreductase activity. In cellular component category, most genes were referred tocellular anatomical entity and intracellular anatomical structure. Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis showed that pathways that involve most of DEGs are metabolic pathways, biosynthesis ofsecondary metabolites, and biosynthesis of amino acids respectively. The microRNA analysis showed thatmiR۱۵۶, miR۱۶۰, and miR۳۹۶ were the candidates that involved the most families. Genetic engineering hasbeen proved to be an efficient approach to the development of salinity-tolerant genotypes, and this approachwill become more powerful as more regulatory elements like key microRNAs associated with salinitytolerance are identified.

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Key words: RNA-seq , microRNA , Gene ontology , Rice , Salinity