An essential aspect of competing in the world market is the quality of the cocoa bean, which is influenced by different factors ranging from genetics to post-harvest processes. The aim of this research was to determine the effect of the maturity stage (2, 3, and 4), genotype (CCN51, ICS95, and TSH565), and geographical location (Algeciras and Garzón, Colombia) of cocoa on the pH and titratable acidity of the pulp and bean, and the fermentation index of the bean during days 0, 3 and 7 of fermentation. The response variables were analyzed through an analysis of variance (ANOVA), and multiple comparisons (pairwise) were made using Tukey's test with a significance level of α = 0.05. Additionally, a longitudinal analysis was carried out as there are measurements over time, and autocorrelation of individuals over time can occur, allowing contrasting the results through another analysis. The results showed that the factor with the strongest influence on the physicochemical characteristics evaluated was the genotype, affecting the bean and pulp pH and the fermentation index. Likewise, it was possible to show that, of the three genotypes evaluated, CCN51 stood out for presenting less bean acidity and higher bean pH and fermentation index. The genotype is the factor with the strongest effect during cocoa fermentation. This solves bean quality heterogeneity, the main international marketing problem.
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