A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in theSalmoGenus and the Impact of Selection on Linked Neutral Diversity

Abstract

High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex-and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (p) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout.

Genomic consequences of a recent three‐way admixture in supplemented wild brown trout populations revealed by local ancestry tracts

“…The BWA_MEM program v. 0.7.9 (Li & Durbin, 2010) was used to align reads along Salmo salar genome before calling SNPs for each individual with the pstacks module (using m = 3 and the bounded error model with α = 0.05). We used a previously established reference RAD catalogue constructed by Leitwein et al (2016Leitwein et al ( , 2017 (-catalog in the cstacks module) for T A B L E 1 Number of individuals sampled for the hatchery strain and wild population (N) along with the number of individuals after filtering for missing data (N filtered ) and the number of individuals considered as pure domestic or pure wild with ADMIXTURE (N pure ) see text for details A single representative of each overlapping site was kept with the option-ordered_export in STACKS.…”

“…The inference of local ancestry was performed with ELAI v1.01 (Guan, 2014), which relies on a two-layer hidden Markov model to detect the structure of haplotypes in unrelated individuals. The program was run separately for each of the 40 linkage groups (LG) of the S. trutta linkage map (Leitwein et al, 2017). We took advantage of the strong collinearity between the S. trutta and S. salar genomes (Leitwein et al, 2017) to anchor the 4,000 mapped RAD loci of the brown trout linkage map onto the reference genome of S. salar.…”

“…The program was run separately for each of the 40 linkage groups (LG) of the S. trutta linkage map (Leitwein et al, 2017). We took advantage of the strong collinearity between the S. trutta and S. salar genomes (Leitwein et al, 2017) to anchor the 4,000 mapped RAD loci of the brown trout linkage map onto the reference genome of S. salar. This strategy allowed to determine the relative mapping positions of a large number of additional RAD loci that were not present on the brown trout linkage map, using their relative positions on the Atlantic salmon reference genome.…”

“…However, most of these studies did not take into account the linkage information contained in ancestry blocks, and therefore could not provide estimates of local ancestry and time since introgression (but see Ozerov et al, 2016). Now that extensive genomic resources are available in salmonids, including dense linkage maps (Gagnaire, Pavey, Normandeau, & Bernatchez, 2013;Gonen et al, 2014;Leitwein et al, 2017;Lien et al, 2011;McKinney et al, 2015;Sutherland et al, 2016;Tsai et al, 2016;Brieuc, Waters, Seeb, & Naish, 2014) and reference genomes (Berthelot et al, 2014;Lien et al, 2016), it becomes possible to explore the potential of local ancestry inference for studying the genomic consequences of HMH.…”

Association mapping reveals candidate loci for resistance and anaemic response to an emerging temperature‐driven parasitic disease in a wild salmonid fish

“…This also enabled us to characterize the extent and pattern of LD. Although the species differ in the chromosomes numbers (2n; S. trutta: 80, Atlantic salmon: 54-58), the fine-scale LD patterns are expected to be congruent because of the high synteny between the two species (Leitwein et al, 2017). Finally, (iv), salmonid fishes have undergone a recent genome duplication~60-80 million years ago (Ss4R) (Macqueen & Johnston, 2014) and at least 10% of the Atlantic salmon genome is still in a tetraploid state (Allendorf et al, 2015;Lien et al, 2016;Limborg, Seeb, & Seeb, 2016).…”