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Plants synthesize secondary constitutive and/or induced metabolites following pathogen invasion. Metabolic profiling is a cutting edge technology in systems biology that studies cell function at the biochemical level through quantification of low molecular weight metabolites in order to reveal cell dynamic response to external stimuli. Wheat fusarium head blight (FHB) caused by Fusarium graminearum (FG) is a key disease of wheat causing severe losses to the crop in North America, Europe and China. Breeding for cultivar resistance is considered the most practical way to manage FHB. Development of a cheaper, more rapid, accurate, and high throughput tool for screening FHB resistance is the highest priority for wheat breeders. Thousands of peaks were detected in wheat-FG pathosystem among which 200 resistance related metabolites were identified and linked to their metabolic pathways. Several metabolites of these were antimicrobial, toxin inhibitors/detoxifiers, signaling molecules, and cell wall apposition compounds among which exist potential FHB resistance bio-markers. This book is a useful text for plant pathology students and teachers, FHB researchers and wheat breeders.