Naim Md Darun, Alamin Md, Mosharof Md Parvez, Imtiaj Ahmed, Haque Mollah Md Nurul
Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi, 6205, Bangladesh.
Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, 6205, Bangladesh.
Heliyon. 2024 Nov 14;10(22):e40395. doi: 10.1016/j.heliyon.2024.e40395. eCollection 2024 Nov 30.
The cultivar 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 rice.
This study has been designed by analysis to explore major RNAi genes highlighting their molecular functions, phylogenetic groups, regulatory factors, and other vital characteristics of rice corresponding to OsRNAi genes.
This study has identified 10 DCLs, 21 AGOs, and 7 RDRs as major RNAi proteins of 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, 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 -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 ) 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 rice crop against different stresses.
该品种水稻因其生命周期短（9周）、适应温室条件、易于接受外源基因且拥有可获取的完整基因组序列，成为一种很有前景的新型水稻研究模式，为研究人员提供了有价值的蓝图。然而，其主要的RNA干扰（RNAi）基因家族（DCLs、AGOs、RDRs）尚未得到研究。这些基因家族影响靶标特异性蛋白质编码基因的表达以及生物和非生物胁迫，调控植物的生长发育。
本研究旨在鉴定和表征水稻中的RNAi基因家族。
本研究通过分析来设计，以探索主要的RNAi基因，突出其分子功能、系统发育组、调控因子以及与水稻OsRNAi基因相对应的其他重要特征。
通过BLASTP搜索，本研究已鉴定出10个DCLs、21个AGOs和7个RDRs作为与水稻OsRNAi相对应的主要RNAi蛋白。结构域分析表明，RNase III、PAZ和Piwi结构域与基因沉默过程相关。根据共线性研究，[具体物种]与水稻在33个RNAi基因对中具有最高的同源性，表明它们具有相同的染色体顺序和相似的功能。大多数OsKRNAi蛋白定位于细胞核和叶绿体中，这与基因沉默有关。基因沉默和核糖核酸酶III活性是基因本体（GO）分析中的关键术语，这是基因沉默过程的一部分。基因调控分析确定了一些重要的转录因子，包括参与DNA结合的ERE，以及包括“Osa-MIR168”在内的微小RNA（miRNA），其可提高水稻对稻瘟病的抗性。对OsKRNAi基因中顺式作用调控元件的研究显示了各种关键成分，包括与不同胁迫相关的MBS、W-box、LTR、ABRE、ARE。发现某些基因（如[具体基因]）在雷帕霉素靶标（TOR）中过表达，增加了对病原体的易感性。
本研究的结果可能为进一步开展实验研究以改良水稻作物应对不同胁迫提供有用资源。
