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...
Published in: | G3 Genes|Genomes|Genetics |
---|---|
Main Authors: | , , , , , |
Format: | Text |
Language: | English |
Published: |
Genetics Society of America
2017
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386884/ http://www.ncbi.nlm.nih.gov/pubmed/28235829 https://doi.org/10.1534/g3.116.038497 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:5386884 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:5386884 2023-05-15T15:31:39+02:00 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 Leitwein, Maeva Guinand, Bruno Pouzadoux, Juliette Desmarais, Erick Berrebi, Patrick Gagnaire, Pierre-Alexandre 2017-02-24 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386884/ http://www.ncbi.nlm.nih.gov/pubmed/28235829 https://doi.org/10.1534/g3.116.038497 en eng Genetics Society of America http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386884/ http://www.ncbi.nlm.nih.gov/pubmed/28235829 http://dx.doi.org/10.1534/g3.116.038497 Copyright © 2017 Leitwein et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. CC-BY Investigations Text 2017 ftpubmed https://doi.org/10.1534/g3.116.038497 2017-04-16T00:15:19Z 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. Text Atlantic salmon PubMed Central (PMC) G3 Genes|Genomes|Genetics 7 4 1365 1376 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Investigations |
spellingShingle |
Investigations Leitwein, Maeva Guinand, Bruno Pouzadoux, Juliette Desmarais, Erick Berrebi, Patrick Gagnaire, Pierre-Alexandre 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 |
topic_facet |
Investigations |
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. |
format |
Text |
author |
Leitwein, Maeva Guinand, Bruno Pouzadoux, Juliette Desmarais, Erick Berrebi, Patrick Gagnaire, Pierre-Alexandre |
author_facet |
Leitwein, Maeva Guinand, Bruno Pouzadoux, Juliette Desmarais, Erick Berrebi, Patrick Gagnaire, Pierre-Alexandre |
author_sort |
Leitwein, Maeva |
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_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_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_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 |
publisher |
Genetics Society of America |
publishDate |
2017 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386884/ http://www.ncbi.nlm.nih.gov/pubmed/28235829 https://doi.org/10.1534/g3.116.038497 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386884/ http://www.ncbi.nlm.nih.gov/pubmed/28235829 http://dx.doi.org/10.1534/g3.116.038497 |
op_rights |
Copyright © 2017 Leitwein et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1534/g3.116.038497 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
7 |
container_issue |
4 |
container_start_page |
1365 |
op_container_end_page |
1376 |
_version_ |
1766362185430204416 |