BMC Genomics · 2019

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

Saint-Pé K, Leitwein M, Tissot L, Poulet N, Guinand B, Berrebi P, Marselli G, Lascaux JM, Gagnaire PA, Blanchet S

Saint-Pé K and Leitwein M contributed equally.

The authors develop a SNP marker resource and a low-density panel for the population genetics of brown trout. The tool is tested in several rivers and compared with classical markers to study differentiation and admixture with domestic strains.

The question: How can reproducible genotyping tools, spread across the genome, be built for brown trout?
The approach: Identification of SNPs from RAD sequences, construction of a 192-marker panel, then testing in several rivers.
What the article brings: The work provides a genomic resource and a genotyping tool for brown trout population studies.
The limits: The performance described applies to this panel and the populations tested; it does not automatically extend to other populations or species.

Figures from the article

Fig. 1, Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics — Fig. 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; informative for at least the AT and ME lineages, positions between the first or last 50 bp of RADs (primer design zones), and spaced by at least 3.5 cM)Original caption. Saint-Pé K et al. (2019), BMC Genomics. CC BY 4.0

Fig. 4, Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics — Fig. 4. Plot of informativeness against number of SNPs. 107 SNPs would be equivalent to the 13 microsatellites in terms of informativenessOriginal caption. Saint-Pé K et al. (2019), BMC Genomics. CC BY 4.0

Fig. 5, Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics — Fig. 5. Map of the five river basins and and sampling sites (black dots) used to test for genotyping success. The Seuge and Ône Rivers are part of the Atlantic catchment, therefore naturally harboring AT trout, whereas the Aude, Roya and Doron de Bozel Rivers are part of the Mediterranean catchment, naturally populated with ME lineage. Maps were generated by authors on ArcGis and assembled using InkscapeOriginal caption. Saint-Pé K et al. (2019), BMC Genomics. CC BY 4.0

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

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