Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics

Abstract

Background The 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. Results A 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. Conclusions The novel resources provided here opens new perspectives for universality and genome-wide studies in brown trout populations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5958-9) contains supplementary material, which is available to authorized users.

Genotype‐by‐environment interactions drive the maintenance of genetic variation in a Salmo trutta L. hybrid zone

“…This potential lineage‐related adaptation to cold conditions indicates in our case that despite several generations in sympatry, gene flow has not erased the link between the set of 6 diagnostic markers that were previously designed on the two separate lineages and genes under potential selection (de Lafontaine et al, 2015 ; Fitzpatrick et al, 2020 ; Lamaze et al, 2012 ). Of particular interest is the fact that robe criteria were well correlated to our genotypic score, whereas recent results indicate that such approach may still miss a large part of the recent genetic admixture (Saint‐Pé et al, 2019 ). This indicates that additional investigations of lineage differences regarding adaptation to cold (MED) or warm (ATL) temperatures could produce even more insightful data to further our understanding of intraspecific diversity dynamics in hybrid zones and to understand how thermal environment could control for postzygotic reproductive isolation (Leitwein et al, 2016 ).…”

Inference of Breed Structure in Farm Animals: Empirical Comparison between SNP and Microsatellite Performance

“…If we limit the overview to vertebrates alone, we can distinguish different types of research. Some studies have compared the effectiveness of the two markers: (i) for the purpose of performing kinship analyses [9][10][11][12][13], (ii) to infer diversity parameters e.g., [14,15], and (iii) to analyze genetic relationships between populations [16][17][18][19][20]. This last group is of particular interest for this study as it aims to enrich knowledge about the precise issue of the inference of population genetic structure.…”

“…This last group is of particular interest for this study as it aims to enrich knowledge about the precise issue of the inference of population genetic structure. The studies [16][17][18][19][20] carried out comparative analyses using a few hundred SNPs, mainly due to the limited availability of SNPs markers for the models considered at the time of the investigation. The study by Gärke et al [18] is an exception as it considers 29 microsatellites and 2931 SNPs in chicken, with the aim of determining the number of SNPs required to achieve the same differentiation power as for a given standard set of microsatellites.…”

Brown trout phylogenetics: A persistent mirage towards (too) many species

“…The release of important genomic resources such as the Atlantic salmon (Lien et al, 2016;GenBank: GCA_000233375.4) and brown trout (GenBank: GCA_901001165.1) genomes provide substrates for progress in trout phylogeny. SNPs are accessible in S. trutta, but are mostly used in a population genomics framework (e.g., Andersson et al, 2017;Drywa et al, 2013;Leitwein et al, 2016;Saint-Pé et al, 2019). Jacobs et al (2018) used SNPs to document the divergence in the S.trutta/S.…”