PT  - JOURNAL ARTICLE
AU  - Maeva Leitwein
AU  - Bruno Guinand
AU  - Juliette Pouzadoux
AU  - Erick Desmarais
AU  - Patrick Berrebi
AU  - Pierre-Alexandre Gagnaire
TI  - A dense brown trout (<em>Salmo trutta</em>) linkage map reveals recent chromosomal rearrangements in the <em>Salmo</em> genus and the impact of selection on linked neutral diversity
AID  - 10.1101/094763
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 094763
4099  - http://biorxiv.org/content/early/2016/12/17/094763.short
4100  - http://biorxiv.org/content/early/2016/12/17/094763.full
AB  - 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 socio-economically important species heavily impacted by human activities. A total of 3,977 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 Salmo 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 3,721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) 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.