title: 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 betweenS. truttaand its sister species,S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after theS. salar/S. truttaspeciation 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 inS. truttaat 3721 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.
authors.affiliation: Institut des Sciences de l'Evolution, Unité Mixte de Recherche 5554 CNRS-IRD-EPHE, Université de Montpellier, 34095 Montpellier Cedex 5, France maeva.leitwein.pro@gmail.com.
authors.forename: Maeva
authors.identifier: 0000-0001-5172-0970
authors.initials: M
authors.lastname: Leitwein
authors.affiliation: Institut des Sciences de l'Evolution, Unité Mixte de Recherche 5554 CNRS-IRD-EPHE, Université de Montpellier, 34095 Montpellier Cedex 5, France.|Département Biologie-Ecologie, Université de Montpellier, 34095 Montpellier Cedex 5, France.
authors.forename: Bruno
authors.identifier: 0000-0002-6934-1677
authors.initials: B
authors.lastname: Guinand
authors.affiliation: Institut des Sciences de l'Evolution, Unité Mixte de Recherche 5554 CNRS-IRD-EPHE, Université de Montpellier, 34095 Montpellier Cedex 5, France.
authors.forename: Juliette
authors.initials: J
authors.lastname: Pouzadoux
authors.affiliation: Institut des Sciences de l'Evolution, Unité Mixte de Recherche 5554 CNRS-IRD-EPHE, Université de Montpellier, 34095 Montpellier Cedex 5, France.
authors.forename: Erick
authors.initials: E
authors.lastname: Desmarais
authors.affiliation: Institut des Sciences de l'Evolution, Unité Mixte de Recherche 5554 CNRS-IRD-EPHE, Université de Montpellier, 34095 Montpellier Cedex 5, France.
authors.forename: Patrick
authors.identifier: 0000-0002-9026-4987
authors.initials: P
authors.lastname: Berrebi
authors.affiliation: Institut des Sciences de l'Evolution, Unité Mixte de Recherche 5554 CNRS-IRD-EPHE, Université de Montpellier, 34095 Montpellier Cedex 5, France.
authors.forename: Pierre-Alexandre
authors.identifier: 0000-0002-1908-3235
authors.initials: PA
authors.lastname: Gagnaire
mesh_terms: D000818:Animals; D002503:Centromere / Q000378:metabolism; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics*; D015321:Gene Rearrangement / Q000235:genetics*; D014644:Genetic Variation; D016678:Genome; D011995:Recombination, Genetic / Q000235:genetics; D012641:Selection, Genetic; D026801:Synteny / Q000235:genetics; D014337:Trout / Q000235:genetics*
keywords: RAD markers; Salmo trutta; chromosomal rearrangements; linkage mapping; recombination rate; salmonids