Network-based transcriptome analysis in salt tolerant and salt sensitive maize (Zea mays L.) genotypes

Identification of genes involved in salinity stress tolerance provides deeper insight into molecular mechanisms underlying salinity tolerance in maize. The present study was conducted in the faculty of agriculture of Urmia university, Iran, in 2018, with the aim of identifying genetic differences between two maize genotypes in tolerance to salinity stress, and the results of gene expression were integrated with gene interaction networks. First, two maize genotypes with extreme phenotypic differences in salinity tolerance were identified using phenotypic screening data. Gene expression was studied by RNA-sequencing to unveil molecular mechanisms underlying salinity tolerance differences in two selected maize genotypes (T9: salinity-tolerant; S46: salinity-sensitive). Phosphorylation-dependent signaling processes, ion transportation, oxidation-reduction, glutathione metabolism, and tryptophan metabolism between tolerant and sensitive genotypes were identified as different biological pathways by gene ontology and interaction network analysis on the genes with differential expression. Network analysis identified a motif as a common regulatory element (cis-regulatory element) in the promoter region of genes belonging to the sub-network with phosphorylation and kinase activity. This motif corresponds to a regulatory element known in Arabidopsis which binds a transcription factor with a known role in responding to salinity-stress. By integrating gene expression and interaction network data obtained from different molecular layers, pathways and genes distinguishing in two salinity-tolerant and salinity-sensitive genotypes were identified, These findings can be used in maize breeding and biotechnology programs to improve maize grain yield under salinity stress conditions.