Population genetics and mitogenome decoding of naturalized rainbow trout (Oncorhynchus mykiss) from the Amazonas region, northern Peru

Olano Y.M.; Chuquizuta F.; Calderon M.S.; Bustamante D.E. · Aquaculture (2025) · DOI: 10.1016/j.aquaculture.2024.742059

Resumen

The rainbow trout (Oncorhynchus mykiss) is an important aquaculture species of high commercial interest in the Andean area of Peru; however, information on its genetics and genomics is limited. This study characterized naturalized rainbow trout from the Amazonas Region using an integrative approach (i.e., taxa delimitation methods, phylogeny, population genetics, mitogenome). In total, 11 phylogenetic lineages and 17 haplotypes were genetically identified and five out of each of those were found in the Amazonas region using the D-loop marker, confirming the high genetic differentiation of this species in the small basins of the Amazonas region. This finding is probably a consequence of egg import and frequent introduction (leakage) of genetic material from fish farms in the Amazonas region. These phenomena are likely contributing to genetic diversity by introducing new alleles and haplotypes. Divergent and less divergent locations were identified in this study. These localities are essential for optimizing breeding, managing genetic diversity, and ensuring the health and sustainability of this farmed species in Amazonas region. The mitochondrial genome of rainbow trout exhibited synteny with that of other salmonids. Only minimal differences in mitogenome lengths (i.e., 16,655–16,660 bp) were noted based on the indels in the 12S rRNA, COII, ND4, ND5, ORL, and D-loop genes. Evolutionary topological analysis suggested that the ND4, ND5 and D-loop genes are useful genes for population genetics studies in rainbow trout. Additionally, 148 out of the 668 single nucleotide variants (SNVs) were identified in the mitochondrial genomes of rainbow trout from the Amazonas region. These SNVs can be included as additional markers of mitochondrial origin to genotype naturalized populations of rainbow trout from worldwide. The use of an integrated approach to study naturalized trout allowed us to understand the significant genetic diversity present in the Amazonas region, providing a new perspective for the management of these populations, especially in the context of local aquaculture.

Instituciones: Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas