A set of nuclear DNA markers diagnostic for marble trout, Salmo marmoratus

Single nucleotide polymorphisms (SNPs) have become popular markers for population genetics and conservation applications. The use of SNPs is increasing in studies on salmonid fishes, particularly in Salmo salar and several Oncorhynchus species, but they are used only occasionally in S. trutta and not at all in marble trout (Salmo marmoratus). Marble trout is native to the northern Adriatic basin, but the continued existence of native parental populations has been compromised by the introduction of brown trout (S. trutta) and subsequent introgressive hybridization. On the basis of more than a decade of experience of the marble trout action plan undertaken in Slovenia, it has become clear that for effective population restoration it is of paramount importance to be able to discriminate reliably between members of either species and marble trout-brown trout hybrids. By undertaking sequence analysis of five nuclear genes in the marble and brown trout genomes, we found several species-specific SNPs that appear to be a useful tool for assessing the genetic purity of populations of marble trout. No linkage disequilibrium was detected in any allelic combinations among the five genes examined. Genotyping of species-specific SNPs in these five genes may provide a valuable diagnostic test for molecular assessment of marble trout purity and thus be suitable for management of marble trout populations, especially when combined with initial phenotype-based sorting.