Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout
Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking deg...
Published in: | G3: Genes|Genomes|Genetics |
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Online Access: | https://hal.science/hal-04202604 https://doi.org/10.1534/g3.120.401184 |
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ftccsdartic:oai:HAL:hal-04202604v1 2023-12-17T10:26:37+01:00 Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout Smith, Seth R. Amish, Stephen J. Bernatchez, Louis Le Luyer, Jeremy Wilson, Chris Boeberitz, Olivia Luikart, Gordon Scribner, Kim T. Ecosystèmes Insulaires Océaniens (UMR 241) (EIO) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé Papeete (ILM) Institut de Recherche pour le Développement (IRD) 2020-06 https://hal.science/hal-04202604 https://doi.org/10.1534/g3.120.401184 en eng HAL CCSD Genetics Society of America info:eu-repo/semantics/altIdentifier/doi/10.1534/g3.120.401184 hal-04202604 https://hal.science/hal-04202604 doi:10.1534/g3.120.401184 ISSN: 2160-1836 G3 https://hal.science/hal-04202604 G3, 2020, 10 (6), pp.1929-1947. ⟨10.1534/g3.120.401184⟩ [SDV]Life Sciences [q-bio] info:eu-repo/semantics/article Journal articles 2020 ftccsdartic https://doi.org/10.1534/g3.120.401184 2023-11-18T23:44:12Z Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal homologies between lake trout and other salmonids of varying divergence. The resulting linkage map contains 15,740 single nucleotide polymorphisms (SNPs) mapped to 42 linkage groups, likely representing the 42 lake trout chromosomes. Female and male linkage group lengths ranged from 43.07 to 134.64 centimorgans, and 1.97 to 92.87 centimorgans, respectively. We improved the map by determining coordinates for 41 of 42 centromeres, resulting in a map with 8 metacentric chromosomes and 34 acrocentric or telocentric chromosomes. We use the map to localize the sex determination locus and multiple quantitative trait loci (QTL) associated with intraspecific phenotypic divergence including traits related to growth and body condition, patterns of skin pigmentation, and two composite geomorphometric variables quantifying body shape. Two QTL for the presence of vermiculations and spots mapped with high certainty to an arm of linkage group Sna3, growth related traits mapped to two QTL on linkage groups Sna1 and Sna12, and putative body shape QTL were detected on six separate linkage groups. The sex determination locus was mapped to Sna4 with high confidence. Synteny analysis revealed that lake trout and congener Arctic char (Salvelinus alpinus) are likely differentiated by ... Article in Journal/Newspaper Arctic Salvelinus alpinus Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Arctic G3: Genes|Genomes|Genetics g3.401184.2020 |
institution |
Open Polar |
collection |
Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
[SDV]Life Sciences [q-bio] |
spellingShingle |
[SDV]Life Sciences [q-bio] Smith, Seth R. Amish, Stephen J. Bernatchez, Louis Le Luyer, Jeremy Wilson, Chris Boeberitz, Olivia Luikart, Gordon Scribner, Kim T. Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout |
topic_facet |
[SDV]Life Sciences [q-bio] |
description |
Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal homologies between lake trout and other salmonids of varying divergence. The resulting linkage map contains 15,740 single nucleotide polymorphisms (SNPs) mapped to 42 linkage groups, likely representing the 42 lake trout chromosomes. Female and male linkage group lengths ranged from 43.07 to 134.64 centimorgans, and 1.97 to 92.87 centimorgans, respectively. We improved the map by determining coordinates for 41 of 42 centromeres, resulting in a map with 8 metacentric chromosomes and 34 acrocentric or telocentric chromosomes. We use the map to localize the sex determination locus and multiple quantitative trait loci (QTL) associated with intraspecific phenotypic divergence including traits related to growth and body condition, patterns of skin pigmentation, and two composite geomorphometric variables quantifying body shape. Two QTL for the presence of vermiculations and spots mapped with high certainty to an arm of linkage group Sna3, growth related traits mapped to two QTL on linkage groups Sna1 and Sna12, and putative body shape QTL were detected on six separate linkage groups. The sex determination locus was mapped to Sna4 with high confidence. Synteny analysis revealed that lake trout and congener Arctic char (Salvelinus alpinus) are likely differentiated by ... |
author2 |
Ecosystèmes Insulaires Océaniens (UMR 241) (EIO) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé Papeete (ILM) Institut de Recherche pour le Développement (IRD) |
format |
Article in Journal/Newspaper |
author |
Smith, Seth R. Amish, Stephen J. Bernatchez, Louis Le Luyer, Jeremy Wilson, Chris Boeberitz, Olivia Luikart, Gordon Scribner, Kim T. |
author_facet |
Smith, Seth R. Amish, Stephen J. Bernatchez, Louis Le Luyer, Jeremy Wilson, Chris Boeberitz, Olivia Luikart, Gordon Scribner, Kim T. |
author_sort |
Smith, Seth R. |
title |
Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout |
title_short |
Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout |
title_full |
Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout |
title_fullStr |
Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout |
title_full_unstemmed |
Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout |
title_sort |
mapping of adaptive traits enabled by a high-density linkage map for lake trout |
publisher |
HAL CCSD |
publishDate |
2020 |
url |
https://hal.science/hal-04202604 https://doi.org/10.1534/g3.120.401184 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Salvelinus alpinus |
genre_facet |
Arctic Salvelinus alpinus |
op_source |
ISSN: 2160-1836 G3 https://hal.science/hal-04202604 G3, 2020, 10 (6), pp.1929-1947. ⟨10.1534/g3.120.401184⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1534/g3.120.401184 hal-04202604 https://hal.science/hal-04202604 doi:10.1534/g3.120.401184 |
op_doi |
https://doi.org/10.1534/g3.120.401184 |
container_title |
G3: Genes|Genomes|Genetics |
container_start_page |
g3.401184.2020 |
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1785578338337685504 |