Bioscience Methods 2024, Vol.15, No.3, 102-113 http://bioscipublisher.com/index.php/bm 103 expression of infection-responsive genes in both rice and pathogens, and explores the potential roles of identified genes in disease resistance and susceptibility. This study aims to provide insights into the molecular mechanisms underlying rice-pathogen interactions that can inform the development of disease-resistant rice varieties. 2 Overview of Rice Pathogens 2.1 Major rice pathogens and their economic impact Rice (Oryza sativa L.) is a staple food crop for more than half of the world's population, making it a critical component of global food security. However, rice production is severely threatened by various pathogens, including bacteria, fungi, viruses, and nematodes, which can lead to significant yield losses. Among the bacterial pathogens, Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) are responsible for bacterial blight (BB) and bacterial leaf streak (BLS), respectively, both of which are major diseases affecting rice production worldwide (Khojasteh et al., 2017; Jiang et al., 2020). Fungal pathogens such as Magnaporthe oryzae, which causes rice blast disease, also pose a significant threat, leading to substantial yield reductions (Liu and Wang, 2016). Additionally, the root-knot nematode (RKN), Meloidogyne graminicola, is known to cause extensive yield decline in rice crops (Kumari et al., 2016). The economic impact of these pathogens is profound, as they not only reduce grain yield but also affect the quality of the produce, thereby threatening the livelihood of millions of farmers and the food supply for billions of people (Kazan and Gardiner, 2018; Wei, et al., 2023). 2.2 Host-pathogen interaction mechanisms in rice Understanding the mechanisms of host-pathogen interactions in rice is essential for developing effective disease management strategies. Rice has evolved a multi-layered immune system to combat pathogen invasion. This includes pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI is initiated upon recognition of conserved microbial molecules, while ETI is activated by specific pathogen effectors recognized by resistance (R) genes in the host (Costa, 2012; Liu and Wang, 2016). For instance, the interaction between rice and Xoo involves a series of R genes and their corresponding avirulence (Avr) genes, which play a crucial role in the plant's defense response (Khojasteh et al., 2017; Jiang et al., 2020). Similarly, proteomic studies have identified several proteins involved in rice's defense against Magnaporthe oryzae, including receptor-like kinases (RLKs) and mitogen-activated protein kinases (MAPKs), which are pivotal in signal transduction and defense response. Hormonal pathways, such as those regulated by salicylate, jasmonate, and ethylene, also play significant roles in modulating the plant's defense mechanisms against various pathogens (Kumari et al., 2016). 2.3 Traditional methods for studying rice pathogen interactions Traditional methods for studying rice-pathogen interactions have primarily focused on genetic and genomic approaches. These include the identification and characterization of R genes and their corresponding Avr genes, as well as the use of quantitative trait loci (QTL) mapping to understand the genetic basis of disease resistance (Jiang et al., 2020; Roychoudhury, 2020). Microarray and gene expression studies have been employed to identify differentially expressed genes (DEGs) in response to pathogen infection, providing insights into the molecular mechanisms underlying host-pathogen interactions (Khojasteh et al., 2017). Proteomic analyses have also been instrumental in identifying key proteins involved in the plant's defense response, thereby enhancing our understanding of the complex interactions between rice and its pathogens (Meng et al., 2019; Wei, et al., 2023). These traditional methods have laid the foundation for more advanced transcriptomic and proteomic studies, which continue to unravel the intricate details of rice-pathogen interactions and aid in the development of disease-resistant rice varieties. 3 Transcriptomic Approaches 3.1 Introduction to transcriptomics and its relevance in plant-pathogen studies Transcriptomics, the study of the complete set of RNA transcripts produced by the genome under specific circumstances, has become a pivotal tool in understanding plant-pathogen interactions. This field allows researchers to capture a snapshot of gene expression at a given time, providing insights into the molecular mechanisms underlying these interactions. By analyzing the transcriptome, scientists can identify which genes
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