A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity
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 rearran...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2017-04-01
|
| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.116.038497 |
| _version_ | 1818571334545833984 |
|---|---|
| author | Maeva Leitwein Bruno Guinand Juliette Pouzadoux Erick Desmarais Patrick Berrebi Pierre-Alexandre Gagnaire |
| author_facet | Maeva Leitwein Bruno Guinand Juliette Pouzadoux Erick Desmarais Patrick Berrebi Pierre-Alexandre Gagnaire |
| author_sort | Maeva Leitwein |
| collection | DOAJ |
| description | 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 (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. |
| first_indexed | 2024-12-14T13:54:20Z |
| format | Article |
| id | doaj.art-75636710e45947f7b7020cdb0a00f05b |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-14T13:54:20Z |
| publishDate | 2017-04-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-75636710e45947f7b7020cdb0a00f05b2022-12-21T22:58:53ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362017-04-01741365137610.1534/g3.116.03849729A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral DiversityMaeva LeitweinBruno GuinandJuliette PouzadouxErick DesmaraisPatrick BerrebiPierre-Alexandre GagnaireHigh-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 (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.http://g3journal.org/lookup/doi/10.1534/g3.116.038497linkage mappingSalmo truttasalmonidsRAD markerschromosomal rearrangementsrecombination rate |
| spellingShingle | Maeva Leitwein Bruno Guinand Juliette Pouzadoux Erick Desmarais Patrick Berrebi Pierre-Alexandre Gagnaire A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity G3: Genes, Genomes, Genetics linkage mapping Salmo trutta salmonids RAD markers chromosomal rearrangements recombination rate |
| title | A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity |
| title_full | A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity |
| title_fullStr | A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity |
| title_full_unstemmed | A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity |
| title_short | A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity |
| title_sort | dense brown trout salmo trutta linkage map reveals recent chromosomal rearrangements in the salmo genus and the impact of selection on linked neutral diversity |
| topic | linkage mapping Salmo trutta salmonids RAD markers chromosomal rearrangements recombination rate |
| url | http://g3journal.org/lookup/doi/10.1534/g3.116.038497 |
| work_keys_str_mv | AT maevaleitwein adensebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity AT brunoguinand adensebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity AT juliettepouzadoux adensebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity AT erickdesmarais adensebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity AT patrickberrebi adensebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity AT pierrealexandregagnaire adensebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity AT maevaleitwein densebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity AT brunoguinand densebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity AT juliettepouzadoux densebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity AT erickdesmarais densebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity AT patrickberrebi densebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity AT pierrealexandregagnaire densebrowntroutsalmotruttalinkagemaprevealsrecentchromosomalrearrangementsinthesalmogenusandtheimpactofselectiononlinkedneutraldiversity |