Genomic Analysis (ddRAD‐seq, mtDNA‐CR and LDH‐C1*) of Brown Trout (Salmo trutta L.)

The aim of this research was to characterize the genetic structure of brown trout (Salmo trutta L.) complex populations in 10 river basins in the Aosta Valley (Italy) and neighbouring regions in northern Italy. The markers used were nuclear Lactate Dehydrogenase (LDH-C1*), mtDNA-CR (Control Region) and ddRAD-seq (SNPs). By this way, the degree of hybridization of wild populations with the Atlantic hatchery lineage was calculated. The results of the genetic analyses showed a composite situation in the studied area with different levels of introgression at the sampling sites. The mitochondrial lineages (Atlantic (AT), Mediterranean (ME), Adriatic (AD) and Marmoratus (MA) were present with varying percentages across study sites. For the Vertosan River, a distinctive native population and a level of hybridization close to zero were identified. Data allowed the identification in the Aosta Valley of four cluster units. In the future, within the study area, some interventions to support conservation actions can be envisaged.