A set of SNPs for Salmo trutta and its application in supplementary breeding programs

The conservation and protection of native populations hybridizing with introduced non-native species in many cases depend crucially on supplemental breeding. Two well-known examples are brown trout in the Danubian basin and marble trout in the Adriatic basin. We present a fluorescence-based genotyping system for a set of 47 nuclear DNA SNP markers, of which 37 are specific for Atlantic and Danubian lineages of brown trout or marble trout and which are thus useful for discrimination of these lineages from their hybrids. Applicability of the system was tested on 120 pure individuals and also on two hybrid marble trout populations in the Soča River and two hybrid populations of Danubian brown trout in the Sava River. STRUCTURE analysis of 50 genotyped samples from two Soča River populations revealed the presence of more than 20% pure native marble trout individuals and confirmed the hypothesis that complete admixture between native parental and introduced trout had not yet been reached. On the other hand, non-pure Danubian brown trout individuals were found in two Sava hybrid populations and only seven contained fewer than 15% non-autochthonous Atlantic genes, suggesting establishment of hybrid swarms. Overall, we believe that the described assay represents a suitable tool that can be used worldwide where conservation management of local trout has been affected by introgression of non-native genes from Danubian, marmoratus and Atlantic trout.

► We present a fluorescence-based genotyping system for a set of 47 SNP markers.
► The system was tested on pure, two hybrid marble and two brown trout populations.
► In Soča River complete admixture between different trout has not yet been reached.
► Results of two Sava populations are suggesting establishment of hybrid swarms.
► Described assay represents a suitable tool for conservation of local trout.