tIntroduction of non-indigenous taxa by anthropogenic activities may lead to the generation of hybridforms and cause genetic pollution of native species. Populations of different Salmo species are threatenedin Italy by hybridization and introgression caused by allochthonous lineages introduced since histori-cal times. In particular, Salmo marmoratus is currently sympatric with domestic lineages of Salmo truttain most of its native geographical range and reproductive interfecundity between the two taxa is seri-ously threatening the genetic purity of the endemic species. To fulfill conservation purposes and fisheriesmanagement, an investigation based on single and multilocus DNA fingerprinting was carried out bothto assess marble trout genetic diversity and the method’s amenability to restocking practices. RFLPs(Restriction Fragments Length Polymorphisms) and SNPs (Single Nucleotide Polymorphisms) in mito-chondrial 16 S rDNA, D-loop, and nuclear LDH-C1* sequences were genotyped in more than 350 samplescollected from different hatcheries in Northern Italy. The combination of the three markers allowed theselection of putative pure individuals of S. marmoratus to be submitted to additional highly polymorphicAFLPs (Amplified Fragment Length Polymorphisms) analyses. Additional benefits of AFLPs over othertechniques emerged in connection with their potential power for fish stock identification. In fact, 52%of all analyzed samples were potentially pure marble trout, 4% were pure Atlantic trout and 44% werehybrids showing different combinations of haplotypes/genotypes. The combined approach demonstratedimproved resolution to reveal hybridization not detected by classical diagnostic markers, and to selectbreeders for reintroduction programs.
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