Major components of RNAi gene families in Oryza sativa cultivar Kitaake: In-silico discovery and characterization

Abstract

Background: The Oryza sativa cultivar Kitaake is a promising new model rice for research due to its short life cycle (9 weeks), adaptability to greenhouse conditions, readily accepts foreign genes, and its complete genome sequence is accessible, providing a valuable blueprint for researchers. However, its major RNA interference (RNAi) gene families (DCLs, AGOs, RDRs) have not yet been studied. These gene families influence target-specific protein-coding gene expression and biotic and abiotic stresses, regulating plant growth and development. Objectives: This study aims to identify and characterize RNAi gene families from the Kitaake rice. Methods: This study has been designed by in-silico analysis to explore major RNAi genes highlighting their molecular functions, phylogenetic groups, regulatory factors, and other vital characteristics of Kitaake rice corresponding to OsRNAi genes. Results: This study has identified 10 DCLs, 21 AGOs, and 7 RDRs as major RNAi proteins of Kitaake rice corresponding to OsRNAi by BLASTP search. Domain analysis has been revealed the RNase III, PAZ, and Piwi domains are related to gene silencing processes. According to synteny study, Kitaake and rice have the most homology in 33 RNAi gene pairs, suggesting they share a chromosomal order and similar functions. The majority of OsKRNAi proteins have been located in the nucleus and chloroplast, which are related to gene silencing. Gene silencing and ribonuclease III activity are key terms from gene ontology (GO) analysis, which is part of the gene silencing process. Gene regulatory analysis has identified some important transcription factors including ERE, which participates in DNA binding and microRNAs (miRNAs) including 'Osa-MIR168' improves rice resistance to blast disease. The investigation of cis-acting regulatory elements in OsKRNAi genes has shown various crucial components, including MBS, W-box, LTR, ABRE, ARE that are linked with the different stresses. Genes (such as OsKAGO1d) were found to be overexpressed in target of rapamycin (TOR), increasing susceptibility to pathogens. Conclusion: The findings of this study may be useful resources for further experimental investigation on the improvement of Kitaake rice crop against different stresses.

Keywords

• Characterizations
• Integrated bioinformatics approaches
• Kitaake rice
• Regulators
• RNAi genes