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Reference Detail
| Reference | ||
|---|---|---|
| Author | Naim M.D., Alamin M., Mosharof M.P., Imtiaj A., Haque Mollah MN. | |
| Title | Major components of RNAi gene families in <i>Oryza sativa</i> cultivar <i>Kitaake</i>: <i>In-silico</i> discovery and characterization. | |
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Abstract: The <i>Oryza sativa</i> cultivar <i>Kitaake</i> 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. This study aims to identify and characterize RNAi gene families from the <i>Kitaake</i> rice. This study has been designed by <i>in-silico</i> analysis to explore major RNAi genes highlighting their molecular functions, phylogenetic groups, regulatory factors, and other vital characteristics of <i>Kitaake</i> rice corresponding to OsRNAi genes. This study has identified 10 DCLs, 21 AGOs, and 7 RDRs as major RNAi proteins of <i>Kitaake</i> 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, <i>Kitaake</i> 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 <i>cis</i>-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 <i>OsKAGO1d</i>) were found to be overexpressed in target of rapamycin (TOR), increasing susceptibility to pathogens. The findings of this study may be useful resources for further experimental investigation on the improvement of <i>Kitaake</i> rice crop against different stresses. |
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| Journal | Heliyon | |
| Country | Bangladesh | |
| Volume | 10(22) | |
| Pages | e40395 | |
| Year | 2024 | |
| PubMed ID | 39624287 | |
| PubMed Central ID | 11609679 | |
| DOI | 10.1016/j.heliyon.2024.e40395 | |
| URL | - | |
| Relation | ||
| Gene | AGO12 AGO13 AGO14 AGO15 AGO16 AGO17 AGO18 AGO1A AGO1B AGO1C AGO1D AGO2 AGO3 AGO4A AGO4B DCL1 DCL2A DCL3A DCL3B MEL1 PNH1 RDR1 RDR2 RDR3 RDR4 SHL2 SHL4 SHO1 | |
| INSD | - | |
| Strain | Wild Core Collection | - |
| Induced Mutation Lines(NIG Collection) | - | |
| Sterile Seed Strain | - | |
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Lethal Embryo Mutantion Strain |
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Stages in Each Organ - Muant Lines (Gene) |
- | |
| Cultivated Varieties(NIG Collection) | - | |
| Stages in Each Organ | - | |
