The Italian-native Mediterranean brown trout (Salmo ghigii) is a seriously threatened freshwater fish, especially by anthropogenic hybridisation with the domestic strains of Atlantic origin that have been repeatedly released into the wild for angling. A PCR-restriction fragment length polymorphism (RFLP) assay of the diagnostic lactate dehydrogenase chain-1 (LDH-C1) gene sequences has been routinely applied to distinguish exotic from native brown trout lineages and detect Atlantic introgression signals in theMediterranean wild populations.Here,weused dermal swabDNAobtained from 28 wild trout to improve laboratory procedures to genetically characterise trout samples at the LDH-C1gene through (1) a capillary electrophoresis analysis of the RFLP fragments and (2) the optimisation of a diagnostic single nucleotide polymorphism analysable through mini-sequencing approaches. The developed methods were fully consistent with those obtained through the traditional approach, but their analytical process is almost entirely automated and digitalised, thus improving result readability and accuracy in the detection of alien introgressed traces inwild Mediterranean brown trout populations.
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