Prediction of RNA editing sites in maize under salt stress through transcriptomic approaches

Climatic changes pose a continuing danger to food production, impacting people's livelihoods worldwide. Salt and drought stresses have significantly impeded global maize output. RNA editing (RE) is a post-transcriptional process and has a unique function in regulating responses to environmental stimuli. The function of RNA editing sites (RES) in maize plants exposed to salt and water stresses has not been well investigated. In this study, two maize genotypes, sensitive to salt (SS) and resistant to salt (ST) were used. We investigated how salt and water stressors impact RNA editing sites in the whole mRNA derived from the maize nuclear genome. The average alignment rate was 90% for SS and 80% for ST genotypes when compared to the reference genome. Most of the editing events were non-synonymous codon alterations, and the trend in amino acid modifications was mostly hydrophobic. When we compared the root and shoot samples from the treated and control groups, we found that both groups had twelve different types of REs including A/C, A/G (A/I), A/T, C/A, C/G, C/T (C/U), G/A, G/C, G/T, T/A, T/C, and T/G. The treated samples showed an overall improvement in RE efficiency. Gene Ontology analysis showed that the mapped genes participated in several biological processes and molecular activities. The analysis of the whole genome's encoded RNA-edited genes showed that 26 sites were altered from C to T (C to U) in the genes ZemaCp023, ZemaCp001, and Zm00001eb437010. Three A/G (A/I) REs were exclusively linked to ZemaCp001. These results will serve as a foundation for identifying RES in other crops and will also be helpful in the development of salt and water tolerance in maize.