Combinations of distinct molecular markers allow to genetically characterize marble trout (Salmo marmoratus) breeders and stocks suitable for reintroduction plans

• Salmo (trutta) marmoratus is a valuable economic and conservation resource.
• More than 350 samples were genotyped for 16 S rDNA, D-loop, and LDH-C1* genes.
• A subset was also genotyped for highly polymorphic AFLPs.
• AFLPs showed a high resolution power to identify hybrids over other techniques.
• The combined approach is useful to select pure breeders for reintroduction plans.

Introduction of non-indigenous taxa by anthropogenic activities may lead to the generation of hybrid forms and cause genetic pollution of native species. Populations of different Salmo species are threatened in Italy by hybridization and introgression caused by allochthonous lineages introduced since historical times. In particular, Salmo marmoratus is currently sympatric with domestic lineages of Salmo trutta in most of its native geographical range and reproductive interfecundity between the two taxa is seriously threatening the genetic purity of the endemic species. To fulfill conservation purposes and fisheries management, an investigation based on single and multilocus DNA fingerprinting was carried out both to assess marble trout genetic diversity and the method’s amenability to restocking practices. RFLPs (Restriction Fragments Length Polymorphisms) and SNPs (Single Nucleotide Polymorphisms) in mitochondrial 16 S rDNA, D-loop, and nuclear LDH-C1* sequences were genotyped in more than 350 samples collected from different hatcheries in Northern Italy. The combination of the three markers allowed the selection of putative pure individuals of S. marmoratus to be submitted to additional highly polymorphic AFLPs (Amplified Fragment Length Polymorphisms) analyses. Additional benefits of AFLPs over other techniques 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% were hybrids showing different combinations of haplotypes/genotypes. The combined approach demonstrated improved resolution to reveal hybridization not detected by classical diagnostic markers, and to select breeders for reintroduction programs.