Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis)
Growth performance and reduced stress response are traits of major interest in fish production. Growth and stress-related quantitative trait loci (QTL) have been already identified in several salmonid species, but little effort has been devoted to charrs (genus Salvelinus). Moreover, most QTL studie...
Published in: | G3 Genes|Genomes|Genetics |
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ftinraparis:oai:prodinra.inra.fr:214886 2023-05-15T18:10:03+02:00 Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis) Sauvage, Christopher Vagner, Marie Derome, Nicolas Audet, Celine Bernatchez, Louis 2012 application/pdf http://prodinra.inra.fr/ft/E9BD7209-8FE9-4B01-B690-FE30C84C15FC http://prodinra.inra.fr/record/214886 https://doi.org/10.1534/g3.112.001990 eng eng http://creativecommons.org/licenses/by-nd-nc/1.0/ CC-BY-ND-NC G3 - Genes Genomes Genetics 6 (2), 707 - 720. (2012) linkage mapping;QTL detection;single-nucleotide polymorphism;growth;stress response;Salvelinus fontinalis;TROUT ONCORHYNCHUS-MYKISS;QUANTITATIVE TRAIT LOCI;SALMON SALMO-SALAR;INFECTIOUS PANCREATIC NECROSIS;RAINBOW-TROUT;BODY-WEIGHT;SEXUAL-MATURATION;GENOME;ARCHITECTURE;POPULATIONS ARTICLE 2012 ftinraparis https://doi.org/10.1534/g3.112.001990 2017-03-21T23:23:37Z Growth performance and reduced stress response are traits of major interest in fish production. Growth and stress-related quantitative trait loci (QTL) have been already identified in several salmonid species, but little effort has been devoted to charrs (genus Salvelinus). Moreover, most QTL studies to date focused on one or very few traits, and little investigation has been devoted to QTL identification for gene expression. Here, our objective was to identify QTL for 27 phenotypes related to growth and stress responses in brook charr (Salvelinus fontinalis), which is one of the most economically important freshwater aquaculture species in Canada. Phenotypes included 12 growth parameters, six blood and plasma variables, three hepatic variables, and one plasma hormone level as well as the relative expression measurements of five genes of interest linked to growth regulation. QTL analysis relied on a linkage map recently built from S. fontinalis consisting of both single-nucleotide polymorphism (SNP, n = 266) and microsatellite (n = 81) markers in an F-2 interstrain hybrid population (n = 171). We identified 63 growth-related QTL and four stress-related QTL across 18 of the 40 linkage groups of the brook charr linkage map. Percent variance explained, confidence interval, and allelic QTL effects also were investigated to provide insight into the genetic architecture of growth-and stress-related QTL. QTL related to growth performance and stress response that were identified could be classified into two groups: (1) a group composed of the numerous, small-effect QTL associated with some traits related to growth (i.e., weight) that may be under the control of a large number of genes or pleiotropic genes, and (2) a group of less numerous QTL associated with growth (i.e., gene expression) and with stress-related QTL that display a larger effect, suggesting that these QTL are under the control of a limited number of genes of major effect. This study represents a first step toward the identification of genes potentially linked to phenotypic variation of growth and stress response in brook charr. The ultimate goal is to provide new tools for developing Molecular Assisted Selection for this species. Article in Journal/Newspaper Salmo salar Institut National de la Recherche Agronomique: ProdINRA Canada G3 Genes|Genomes|Genetics 2 6 707 720 |
institution |
Open Polar |
collection |
Institut National de la Recherche Agronomique: ProdINRA |
op_collection_id |
ftinraparis |
language |
English |
topic |
linkage mapping;QTL detection;single-nucleotide polymorphism;growth;stress response;Salvelinus fontinalis;TROUT ONCORHYNCHUS-MYKISS;QUANTITATIVE TRAIT LOCI;SALMON SALMO-SALAR;INFECTIOUS PANCREATIC NECROSIS;RAINBOW-TROUT;BODY-WEIGHT;SEXUAL-MATURATION;GENOME;ARCHITECTURE;POPULATIONS |
spellingShingle |
linkage mapping;QTL detection;single-nucleotide polymorphism;growth;stress response;Salvelinus fontinalis;TROUT ONCORHYNCHUS-MYKISS;QUANTITATIVE TRAIT LOCI;SALMON SALMO-SALAR;INFECTIOUS PANCREATIC NECROSIS;RAINBOW-TROUT;BODY-WEIGHT;SEXUAL-MATURATION;GENOME;ARCHITECTURE;POPULATIONS Sauvage, Christopher Vagner, Marie Derome, Nicolas Audet, Celine Bernatchez, Louis Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis) |
topic_facet |
linkage mapping;QTL detection;single-nucleotide polymorphism;growth;stress response;Salvelinus fontinalis;TROUT ONCORHYNCHUS-MYKISS;QUANTITATIVE TRAIT LOCI;SALMON SALMO-SALAR;INFECTIOUS PANCREATIC NECROSIS;RAINBOW-TROUT;BODY-WEIGHT;SEXUAL-MATURATION;GENOME;ARCHITECTURE;POPULATIONS |
description |
Growth performance and reduced stress response are traits of major interest in fish production. Growth and stress-related quantitative trait loci (QTL) have been already identified in several salmonid species, but little effort has been devoted to charrs (genus Salvelinus). Moreover, most QTL studies to date focused on one or very few traits, and little investigation has been devoted to QTL identification for gene expression. Here, our objective was to identify QTL for 27 phenotypes related to growth and stress responses in brook charr (Salvelinus fontinalis), which is one of the most economically important freshwater aquaculture species in Canada. Phenotypes included 12 growth parameters, six blood and plasma variables, three hepatic variables, and one plasma hormone level as well as the relative expression measurements of five genes of interest linked to growth regulation. QTL analysis relied on a linkage map recently built from S. fontinalis consisting of both single-nucleotide polymorphism (SNP, n = 266) and microsatellite (n = 81) markers in an F-2 interstrain hybrid population (n = 171). We identified 63 growth-related QTL and four stress-related QTL across 18 of the 40 linkage groups of the brook charr linkage map. Percent variance explained, confidence interval, and allelic QTL effects also were investigated to provide insight into the genetic architecture of growth-and stress-related QTL. QTL related to growth performance and stress response that were identified could be classified into two groups: (1) a group composed of the numerous, small-effect QTL associated with some traits related to growth (i.e., weight) that may be under the control of a large number of genes or pleiotropic genes, and (2) a group of less numerous QTL associated with growth (i.e., gene expression) and with stress-related QTL that display a larger effect, suggesting that these QTL are under the control of a limited number of genes of major effect. This study represents a first step toward the identification of genes potentially linked to phenotypic variation of growth and stress response in brook charr. The ultimate goal is to provide new tools for developing Molecular Assisted Selection for this species. |
format |
Article in Journal/Newspaper |
author |
Sauvage, Christopher Vagner, Marie Derome, Nicolas Audet, Celine Bernatchez, Louis |
author_facet |
Sauvage, Christopher Vagner, Marie Derome, Nicolas Audet, Celine Bernatchez, Louis |
author_sort |
Sauvage, Christopher |
title |
Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis) |
title_short |
Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis) |
title_full |
Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis) |
title_fullStr |
Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis) |
title_full_unstemmed |
Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis) |
title_sort |
coding gene snp mapping reveals qtl linked to growth and stress response in brook charr (salvelinus fontinalis) |
publishDate |
2012 |
url |
http://prodinra.inra.fr/ft/E9BD7209-8FE9-4B01-B690-FE30C84C15FC http://prodinra.inra.fr/record/214886 https://doi.org/10.1534/g3.112.001990 |
geographic |
Canada |
geographic_facet |
Canada |
genre |
Salmo salar |
genre_facet |
Salmo salar |
op_source |
G3 - Genes Genomes Genetics 6 (2), 707 - 720. (2012) |
op_rights |
http://creativecommons.org/licenses/by-nd-nc/1.0/ |
op_rightsnorm |
CC-BY-ND-NC |
op_doi |
https://doi.org/10.1534/g3.112.001990 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
2 |
container_issue |
6 |
container_start_page |
707 |
op_container_end_page |
720 |
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1766182777576751104 |