Genomic analyses for traceability: the trout of the Orb
The Mediterranean basin of the Orb (Hérault), a river in southern France covering 1,580 km², has been restocked since the late 1960s with domestic brown trout (Salmo trutta) of Atlantic and Mediterranean origin, to increase the local Mediterranean populations for recreational fishing.
In Leitwein et al. (2018) (opens in a new tab), 75,684 mapped SNPs obtained by ddRAD-seq described the contributions of Atlantic and Mediterranean domestic strains to wild populations in the Orb basin.
This identified individuals of Atlantic domestic origin (fish-farm escapees) in the Gravezon river, individuals of Mediterranean domestic origin in the Mare river, and hybrid individuals carrying Atlantic and Mediterranean domestic alleles in all three wild rivers (Figure 1).
Figure (opens in a new tab)The age of the introductions
Studying the Atlantic and Mediterranean domestic haplotypes (segments) also allowed us to estimate the age of the introductions in each of the three rivers.
Atlantic domestic individuals were introduced on average 24.01 generations ago in the Gravezon river, 22.31 generations ago in the Mare river and 30.9 generations ago in the Orb river (Figure 2).
Similarly, the introduction of Mediterranean domestic trout was estimated at 11.51 generations ago in the Gravezon river, 25.07 generations in the Mare and 23.23 in the Orb (Figure 2).
Figure (opens in a new tab)Developing genomic tools: a SNP resource and a targeted panel
Saint-Pé et al. (2019) (opens in a new tab) identified a resource of 12,204 SNPs distributed across the 40 linkage groups of brown trout (Salmo trutta). From that resource, they developed a low-density panel of 192 SNPs (Figure 3).
The panel was evaluated in 1,862 individuals from five rivers. It provides a reproducible and cost-effective genotyping tool for population genetic studies.
In the populations tested, it distinguishes Atlantic and Mediterranean lineages and supports investigation of admixture with domestic strains.
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