ArticleBMC genomics2019
Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Genetic consequences of improved river connectivity in brown trout (Evolutionary applications · 2024Article
- A multiplexed plant-animal SNP array for selective breeding and species conservation applications.G3 (Bethesda, Md.) · 2023Article
- Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations.Animals : an open access journal from MDPI · 2023Review
- A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales.Journal of fish biology · 2023Article
- Phenology and plasticity can prevent adaptive clines in thermal tolerance across temperate mountains: The importance of the elevation-time axis.Ecology and evolution · 2022Article
- Article
- Genomic Hatchery Introgression in Brown Trout (Genes · 2022Article
- Comparison of seven SNP calling pipelines for the next-generation sequencing data of chickens.PloS one · 2022Article
- Genotype-by-environment interactions drive the maintenance of genetic variation in aEvolutionary applications · 2021Article
- Article
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10 authors.
Funding
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.
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