Cocoa bean quality depends mainly on genetic material, edaphoclimatic factors and post-harvest processes such as fermentation. The impact of the fermentation process on the chemical and functional composition of different cocoa clones grown in southern Colombia was analyzed. A factorial design with repeated measures over time was used to analyze the effect of clone and fermentation time on chemical characteristics (bromatology, phenolic compounds and antioxidant activity). The bromatological characteristics showed significant differences between clones and fermentation time. Clones EET-8 and CCN-51 showed higher contents of acidity (0.51%), fat (63.61%), protein (12.85%) and carbohydrates (1.63 mg g−1). Moisture, acidity and sucrose increased their values between day 4 and day 6 of fermentation (p < 0.05). Phenolic compounds and antioxidant activity had significant differences between clones, where clones CCN-51 and ICS-95 had high contents of phenols (64.56 mg g−1), flavonoids (3.30 mg g−1) and DPPH reducing capacity (325.55 µmol g−1). In this sense, we consider the FSV-41 clone as the major grain quality index based on the results of chemical composition at the bromatological level, antioxidant activity and phenolic compounds.
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