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Brown spot disease, caused by Bipolaris oryzae, is a dominant lethal rice disease that causes qualitative and quantitative crop damage. The current study sought to identify various histological and metabolic changes that occur during brown spot development in susceptible rice plants. We present a conceptual framework that shows B. oryzae suppresses the production of immune-related metabolites in a susceptible cultivar, PR 124 using a comparative metabolomics approach. Un-inoculated rice leaves have an epidermis followed by cortex parenchyma with large intercellular spaces, and no fungal hyphae or distortion were found. Following pathogen inoculation, fungus hyphae grow intercellularly in photosynthetic areas and intracellularly in the bundle sheath, resulting in the microcracks on the surface of the rice leaf. Cellular depositions could have produced the clogging, which disrupted water channels and …