Abstract Cacao stands as a vital export commodity, necessitating consistent high-quality cocoa beans to meet market demands. Controlled hybridizations for genetic enhancement offer a pathway to improve bean quality and to increase genetic variation. We elucidated the phenotypic variation of pod characteristics in F₁ progenies generated from four distinct cross combinations and its molecular characterization. Phenotypic analysis revealed notable outcomes within progenies of TSH858xDR1 cross, demonstrating high average pod weight and a beans-per-100g count aligning with grades AA/A. Among these progenies, 5 − 1 (2), showcased several advantageous traits including the highest weight of a single dried bean and the lowest pod index reflecting large bean sizes. Molecular characterization revealed that all the F₁ progenies were different from each other, confirming the differences in phenotypic traits were strongly influenced by genetic variation. These findings underscore the efficacy of intentional crosses which are crucial for genetic improvement.
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