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

Keoni Saint-Pé (1) , Maeva Leitwein (2, 3) , Laurence Tissot (4) , Nicolas Poulet (5) , Bruno Guinand (2) , Patrick Berrebi (2) , Geoffrey Marselli (1) , Jean-Marc Lascaux (6) , Pierre-Alexandre Gagnaire (2) , Simon Blanchet (7, 1)

1 SETE - Station d'écologie théorique et expérimentale
2 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
3 ULaval - Université Laval [Québec]
4 EDF R&D LNHE - Laboratoire National d’Hydraulique et Environnement
5 Écologie des organismes aquatiques
6 Etudes et Conseils en Gestion de l'Environnement Aquatique - ECOGEA (FRANCE)
7 EDB - Evolution et Diversité Biologique

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.

Mots clés: Conservation; Management; Population genomics; Microarray; Admixture

Domaines: Biodiversité et Ecologie; Génétique des populations [q-bio.PE]; Génétique animale; Sciences de l'environnement

Keoni Saint-Pé, Maeva Leitwein, Laurence Tissot, Nicolas Poulet, Bruno Guinand, et al.. Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics. BMC Genomics, 2019, 20 (1), ⟨10.1186/s12864-019-5958-9⟩. ⟨hal-02395980⟩