In fruit tree breeding, selection indices are used to identify the genotypes that combine desirable commercial and non-commercial characteristics. As Theobroma grandiflorum is generally cultivated in agroforestry systems (AFS), there is a need to develop cultivars that are adapted to such environments. In this study, the objective was to select the most promising genotypes for their future use in AFS based on the additive index, a pioneering method for this crop. The trial was carried out for 12 years in an agroforestry system in the municipality of Tomé-Açu, Pará State, Brazil. The 16 evaluated clones were completely randomised with a variable number of repetitions. The average number of fruits produced as well as the morpho-agronomic characteristics of the fruits were analysed. Mixed linear models were used to estimate the components of variance and predict the genotypic values. The genetic correlation between the variables was estimated, and the selection of genotypes was based on the additive index, with a positive orientation of all variables except the thickness of the fruit shells and the weight of the fruits. Clones 42, 44, 46, 47, 57, 61, and 64 performed well for all the analysed variables, resulting in a selection gain of 7.3% and low incidence rates of witches’ broom disease. These genotypes can be made available to producers in the form of clones for use in AFS and can further be included in future hybridisations in T. grandiflorum breeding.
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