In Amazonia, small-oriented family businesses or communities cultivate freshwater organisms as a source of income. Although effective management is fundamental for optimizing cultivated stocks, Amazonian aquaculture belittles the importance of genetic diversity, relying primarily on phenotypical characteristics during breeders’ selection. To provide a “proof of concept” built on the premise that implementing modern technologies is crucial to optimizing fish stocks in rural Amazonian fish farms, we conducted a pilot study assessing genetic diversity on cultivated Piaractus brachypomus from Caquetá, Colombia. We used mitochondrial control region (CR) sequences to evaluate heterogeneity. Our data revealed low genetic diversity and suggested that most sampled individuals probably originated from a single maternal lineage. Haplotype diversification resulted from discrete point mutations not associated with geographical location. Polymorphisms accumulate in non-conserved CR regions, yet the most divergent haplotypes display mutations in conserved CR sequences with roles in mitochondrial metabolisms and proliferation. Overall, our results indicate a need in the local industry to design breeding strategies to enhance diversity to avoid deleterious effects caused by inbreeding and domestication.
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