Bioscience Methods 2024, Vol.15, No.3, 102-113 http://bioscipublisher.com/index.php/bm 102 Research Report Open Access Transcriptomic Approaches to Studying Rice Pathogen Interactions Yuming Huang School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China Corresponding email: hym@xmu.edu.cn Bioscience Methods, 2024, Vol.15, No.3 doi: 10.5376/bm.2024.15.0012 Received: 29 Mar., 2024 Accepted: 22 May, 2024 Published: 02 Jun., 2024 Copyright © 2024 Huang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Huang Y.M., 2024, Molecular diagnostics: a new era in pet disease detection, Bioscience Methods, 15(3): 102-113 (doi: 10.5376/bm.2024.15.0012) Abstract Understanding the intricate interactions between rice (Oryza sativa) and its pathogens is crucial for developing effective disease management strategies. Transcriptomic approaches have significantly advanced our knowledge in this area by enabling comprehensive profiling of gene expression during infection. This study leverages high-quality RNA sequencing and other transcriptomic techniques to explore the dynamic interactions between rice and various pathogens, including the rice blast fungus (Magnaporthe oryzae) and the Rice black-streaked dwarf virus (RBSDV). Key findings include the identification of differentially expressed mRNAs and long non-coding RNAs (lncRNAs) that play essential roles in rice's defense mechanisms, as well as novel microRNAs (miRNAs) that regulate pathogen resistance genes. Additionally, tissue-specific expression patterns of pathogenicity genes and miRNAs were observed, providing deeper insights into the dual-epidemics of blast disease. These transcriptomic analyses offer a valuable resource for understanding the molecular mechanisms underlying rice-pathogen interactions and pave the way for developing improved disease-resistant rice varieties. Keywords Rice-pathogen interactions; Transcriptomics; Magnaporthe oryzae; Long non-coding RNAs (lncRNAs); MicroRNAs (miRNAs) 1 Introduction Rice (Oryza sativa L.) is a staple food crop that feeds more than half of the world's population. However, the stability and growth of rice yield are facing threats from a variety of biotic and abiotic factors (Yang, 2024). Among them, various pathogens, including bacteria, fungi, and viruses, which lead to significant yield losses. Bacterial blight (BB) and bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) respectively, are particularly detrimental (Jiang et al., 2020). Additionally, fungal diseases such as rice blast, caused by Magnaporthe oryzae, and other fungal pathogens like Pyricularia oryzae, Ustilaginoidea virens, and Rhizoctonia solani, pose severe threats to rice crops globally (Liu et al., 2014; He et al., 2022). Understanding the interactions between rice and these pathogens is crucial for developing effective disease management strategies. The study of transcriptomic responses in rice during pathogen interactions has provided significant insights into the molecular mechanisms underlying plant defense and pathogen attack. Transcriptomics, which involves the comprehensive analysis of RNA transcripts, allows researchers to identify infection-responsive genes and understand their roles in disease resistance and susceptibility (Sarki et al., 2020). For instance, transcriptomic analyses have revealed the upregulation of specific genes in rice that are involved in defense responses, such as pathogenesis-related proteins and phytoalexin biosynthetic genes, during interactions with pathogens (Kawahara et al., 2012). Moreover, the identification of pathogen-associated molecular patterns (PAMPs) and effector-triggered immunity (ETI) has advanced our understanding of the complex signaling networks that govern plant immunity (Liu et al., 2014; Liu and Wang, 2016). These insights are essential for developing new strategies to enhance disease resistance in rice through genetic and genomic approaches. This study utilizes transcriptomic approaches to investigate the interactions between rice and its pathogens. By analyzing the gene expression profiles of both rice and its pathogens during infection, this study identifies key genes and pathways involved in the defense response and pathogen virulence; focuses on the characterize of the transcriptomic changes in rice during interactions with bacterial and fungal pathogens; identifies and analyzes the
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