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Theobroma cacao produces cocoa beans, an essential ingredient for the production of chocolate. This book recapitulates the research focusing on enhancing disease resistance in Theobroma cacao via two approaches: The first approach targeted improved understanding of the pathogenicity mechanisms of Moniliophthora perniciosa, the causal agent of witches broom disease because of its economical impact in South America and the potential threat to unaffected areas in other continents. This approach involved identifying tomato varieties that differentially interact with M. perniciosa to study mechanisms of pathogenesis and resistance toward the goal of making tomato as a surrogate model for cacao witches broom. The second approach utilizes T. cacao over-expressing an endochitinase gene which conferred higher resistance to the fungal pathogen Colletotrichum gloeosporioides. This book targets students and researchers in the field of plant pathology and genetics interested in biotechnology of tropical plants.