Comparative biochemical and transcriptomic profiling of açaí and cacao fruits from Eastern Amazon agroforestry systems

Agroforestry is an agricultural practice that combines production with sustainability. In the Eastern Amazon region, this system is used to harvest native fruits such as açaí and cacao. However, different management strategies may be associated with contrasting biochemical and molecular characteristics of these fruits. To evaluate these differences, a comparative observational analysis of açaí pulps and cacao seeds with adhering arils was performed using samples from two neighboring agroforestry systems in Tomé-Açu (Pará, Brazil), with one farm representing an organic management regime (AFS19) and the other representing a conventional management regime (AFS27). The analysis focused on trace element composition, metabolic diversity, and gene expression. The elemental composition of the fruits was broadly similar, although açaí from AFS19 had 35% and 38% higher concentrations of phosphorus and copper, respectively, while cacao from AFS27 had 17%–30% higher concentrations of calcium, manganese, magnesium, and sulfur. The metabolic profiles of both açaí and cacao from AFS19 were more diverse and included several putative compounds, such as apigenin and esculin, tentatively annotated only in samples from AFS19. Transcriptomic data showed that açaí pulps from AFS19 had higher expression of genes associated with antioxidative processes and stress resistance, whereas AFS27 showed higher expression of genes related to ripening, proteolysis, and flavonoid biosynthesis. In cacao seeds, AFS19 showed higher expression of transcripts associated with seed protection and carbohydrate metabolism on reserve mobilization, while AFS27 showed higher expression of genes related to pathogen resistance, seed coating, and maturation. Overall, the combined analysis revealed distinct biochemical and transcriptomic profiles between the two agroforestry systems, providing comparative data on fruit characteristics associated with contrasting management regimes in tropical agroforestry systems.