- Development of a large SNPs resource and a low-density SNP array for brown trout ( Salmo trutta ) population genetics. - Background: The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. - 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. - 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. - Conclusions: The novel resources provided here opens new perspectives for universality and genome-wide studies in brown trout populations.. - The brown trout (Salmo trutta) is one of the most wide- spread freshwater fish species in Eurasia, and it has been widely introduced in both the southern and northern hemispheres [1]. - As part of the Salmonidae family, it is a scientifically interesting species because of its diversity in terms of ecology, life history strategies and habitat use. - The brown trout is also 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 intro- duction [6]. - Because this species is strongly associated to human interests, wild brown trout populations are widely managed, either to sustain attractive leisure activ- ities such as recreational angling or to conserve declin- ing and/or emblematic populations. - Moreover, the brown trout has been domesticated since the nineteenth. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article. - Instead of positive expected effects of these stocking activities, most have proven to have negative long term effects on wild brown trout populations in part because of the re- duced fitness brought by hatchery fish in wild popula- tions, and the loss of local genetic heritage caused by the replacement of local wild populations with genetically homogeneous hatchery strains [11–14].. - The brown trout presents high levels of phenotypic and genetic polymorphism, with seven main mitochondrial (mtDNA) lineages with various geographical extents being generally recognized. - However, diversity patterns in brown trout have also been locally in- fluenced by stocking practices that mostly relied on Euro- pean hatchery strains of AT origin [25] to supplement local populations, with the exception of a few local strains stemming from local populations [26 – 28].. - For instance, assignment tests, fine-scale population structure, kinship analyses and genome-wide surveys [32 – 34] enable to monitor populations effectively, and have high potential applications for conservation and manage- ment in salmonids, including the brown trout . - In particular, Linløkken [58] developed 3781 SNPs to analyse genetic differences between wild and hatchery brown trout in a tributary of Lake Savalen in central Norway. - This latter resource provides a novel baseline for the development of mapped SNPs that may be of prime interest for studies on brown trout population genetics across a wide spatial range.. - The aim of this study was to develop a genome-wide, mapped and universal set of SNPs for the brown trout for both Atlantic and Mediterranean lineages (AT and ME lineages. - By taking advantage of the new genomic resource available for brown trout we developed a panel of 12,204 RADs containing 1 or 2 polymorphic SNPs evenly spread across the genome structured in 40 chromosomes, and ancestry informative for at least two of the main brown trout lineages, the At- lantic and the Mediterranean lineages. - Development of the large SNPs resource and characteristics of the low-density SNP array. - One estimate of the local recombination rate for each SNP (i.e. - one index of the relative power of markers for LD-based mapping ap- proaches) is provided in Additional file 1: S1 and S2.. - Genotyping success of the low-density SNPs array Thirty of the 192 SNPs (among which a mitochondrial marker) that were initially genotyped in the five water- sheds did not amplify, suggesting primers failure to properly bind their target DNA site. - For the loci that successfully amplified, the overall genotyping success was high, with less than 1% of missing data per individ- ual, irrespective of the river basin and the lineage (Table 1). - 1 Positions on the brown trout linkage map of the 12204 RADs (a. - containing one or two SNPs with MAF ≥ 5% based on all individuals (AT + ME) and positions between the first or last 30 bp of the RAD with no undetermined nucleotides), and of the 245 SNPs (b. - out of the 162 SNPs that were successfully genotyped in that portion of our work (Table 1). - Efficiency of the low-density SNPs array. - We found that the informativeness of these 92 SNPs is actually equivalent to that of 10 of the microsatellites (Fig. - The SNP panel developed here was shown to be efficient to study the population genetics of Atlantic and Medi- terranean brown trout lineages from Western Europe, which gathered a huge number of studies in the past de- cades [60–62]. - Development of a large variation map for population genomic studies in brown trout. - Second, we chose a relatively high MAF because this panel of SNPs is primarily de- signed for studying populations for most of the species range. - Removing loci displaying selection is thus up to the users of the resource, depending on the aim of the study. - Therefore, the 12,204 RAD panel is a promising tool for genome wide studies on brown trout. - [15]) or re- mote populations inhabiting at the edges of the species’. - Tests of the low-density SNP array. - Hence, the strong advantage of a SNP panel of this type is that it ensures a better representativeness of the entire genome of the brown trout. - The SNP panel presented here appears as a novel tool to study diverse aspects of population genetics in the brown trout. - We hope that it will be useful to the population ge- neticists’ community working on brown trout and call for future studies across the species ’ range.. - trutta linkage map using an intermediate step of physical mapping to the Atlantic salmon refer- ence genome: using their relative positions on the At- lantic salmon reference genome, it was possible to determine the relative mapping positions of a large number of additional RAD loci that were not present on the brown trout linkage map [59].. - 5 Map of the five river basins and and sampling sites (black dots) used to test for genotyping success. - highly polymorphic, (ii) mapped on the linkage map, and (iii) present in the two brown trout lineages. - Development of the low-density SNP array. - Moreover, SNPs were selected to be informative for population genetics analyses of brown trout populations from at least the AT and ME lineages (sensu Bernatchez [15]) from Western Europe. - Finally, we added five mitochondrial SNPs previ- ously used to differentiate among the five main brown trout lineages (mitoDA10Proline, mitoDA10ProlineB, mitoCytoB, mitoATPaseIVA, mitoATPaseIVB. - 5% of the markers present on the SNP array. - Genotyping success of the low-density SNP array. - The sampling sessions were performed in 2016, using a single-pass electrofishing approach from a total of 79 sites (between 8 and 21 sites per river basin, Additional file 1: S5), with an aim of sampling 30 individuals of brown trout per site. - Fin samples were sent to the LGC Genomics com- pany for DNA extraction and multilocus genotyping of the 192 SNPs markers using KASPAR® [87]. - The low-density SNP array was further used for classic population genetic questions in order to compare its effi- ciency with thirteen microsatellite markers previously used in brown trout population genetic studies (e.g. - A total of 190 brown trout individuals were sampled in a small river basin (the Taurion River in the Massif Central Mountains. - We additionally sampled 30 in- dividuals of domestic Atlantic brown trout from a local hatchery used for stocking purposes (the Soueich trout hatchery), to quantify genetic admixture with wild popula- tions from the Taurion basin. - Individuals were assigned to one of the two clusters with the greatest Q-value, provided that value exceeded 0.7 (as in [94. - A higher index indicates a higher informativeness of the set of markers. - RAD data set of 12204 sequences each containing one or two SNPs, with minimum allele frequency of 5% or higher, no SNPs in the first or last 30 bp of the RAD, no unsequenced nucleotides, and which can be positioned on the S. - Map of the Taurion River showing sampling points (black dots). - This work was undertaken at SETE, which forms part of the “ Laboratoire d ’ Excellence ” (LABEX) entitled TULIP (ANR-10-LABX-41), and M. - KSP, ML PAG, and SB wrote the first draft of the manuscript. - Two of the authors are attached to the funding body (Tissot Laurence, EDF. - Poulet Nicolas, AFB), and have contributed to the design of the study, the collection, analysis, and interpretation of data, and in writing the manuscript.. - Brown trout: biology, ecology and management. - Atlantic salmon Salmo salar L., brown trout Salmo trutta L. - Spatial patterns in relations among brown trout (Salmo trutta) distribution, summer air temperature, and stream size in Rocky Mountain streams. - Conservation genetic management of brown trout (Salmo trutta) in Europe. - Stocking impact and allozyme diversity in brown trout from Mediterranean southern France. - Quantitative ecology and the brown trout. - Estimating the long-term effects of stocking domesticated trout into wild brown trout (Salmo trutta) populations: an approach using microsatellite DNA analysis of historical and contemporary samples. - 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