Résumé
High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. Insalmonids, a complex rediploidization process consecutive to an ancient whole genome duplication eventmakes linkage maps of prime importance for investigating the evolutionary history of chromosomerearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmotrutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRADmarkers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombinationdistances obtained from two family crosses. Performing map comparison betweenS. truttaand its sisterspecies,S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion andfissionevents that occurred after theS. salar/S. truttaspeciation happened in the Atlantic salmon branch, whereasthe brown trout remained closer to the ancestral chromosome structure. Using the strongly conservedsynteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genomesequence to estimate the local recombination rate inS. truttaat 3721 loci. A significant positive correlationbetween recombination rate and within-population nucleotide diversity (p) was found, indicating thatselection constrains variation at linked neutral sites in brown trout. This new high-density linkage mapprovides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies inbrown trout