Abstract
BackgroundThe brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are microsatellites and mitochondrial markers that lack replicability among laboratories, and a large genome coverage. An alternative that may be particularly efficient and universal is the development of small to large panels of Single Nucleotide Polymorphism markers (SNPs). Here, we used Restriction site Associated DNA sequences (RADs) markers to identify a set of 12,204 informative SNPs positioned on the brown trout linkage map and suitable for population genetics studies. Then, we used this novel resource to develop a cost-effective array of 192 SNPs (96 × 2) evenly spread on this map. This array was tested for genotyping success in five independent rivers occupied by two main brown trout evolutionary lineages (Atlantic -AT- and Mediterranean -ME-) on a total of 1862 individuals. Moreover, inference of admixture rate with domestic strains and population differentiation were assessed for a small river system (the Taurion River, 190 individuals) and results were compared to a panel of 13 microsatellites.ResultsA high genotyping success was observed for all rivers (< 1% of non-genotyped loci per individual), although some initially used SNP failed to be amplified, probably because of mutations in primers, and were replaced. These SNPs permitted to identify patterns of isolation-by-distance for some rivers. Finally, we found that microsatellite and SNP markers yielded very similar patterns for population differentiation and admixture assessments, with SNPs having better ability to detect introgression and differentiation.ConclusionsThe novel resources provided here opens new perspectives for universality and genome-wide studies in brown trout populations.
Highlights
The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed
By taking advantage of the new genomic resource available for brown trout [14, 51, 59], we developed a panel of 12,204 Restriction site associated DNA (RAD) containing 1 or 2 polymorphic Single nucleotide polymorphisms (SNP) evenly spread across the genome structured in 40 chromosomes, and ancestry informative for at least two of the main brown trout lineages, the Atlantic and the Mediterranean lineages
Development of the large SNPs resource and characteristics of the low-density SNP array After applying filters, we identified a RAD data set of 12, 204 sequences each containing one or two SNPs that met our specifications and that are made readily available to the scientific community
Summary
The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. We used Restriction site Associated DNA sequences (RADs) markers to identify a set of 12,204 informative SNPs positioned on the brown trout linkage map and suitable for population genetics studies. We used this novel resource to develop a cost-effective array of 192 SNPs (96 × 2) evenly spread on this map. The brown trout is an economically major species in terms of farming, net fishing (for the sea-run form), and expenditure in recreational angling [4, 5], partly explaining its worldwide intentional introduction [6] Because this species is strongly associated to human interests, wild brown trout populations are widely managed, either to sustain attractive leisure activities such as recreational angling or to conserve declining and/or emblematic populations.
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