Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis)

• Published in: G3 Genes|Genomes|Genetics
• Main Authors: Sauvage, Christopher, Vagner, Marie, Derôme, Nicolas, Audet, Céline, Bernatchez, Louis
• Other Authors: Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de la MER de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Institut de Biologie Intégrative et des Systèmes Québec (IBIS), Natural Sciences and Engineering Research Council of Canada (NSERC); FQRNT (Fonds Quebecois pour la Recherche, Nature et Technologies)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2012
• Subjects: linkage mapping; QTL detection; single-nucleotide polymorphism; growth; stress response; TROUT ONCORHYNCHUS-MYKISS; INFECTIOUS PANCREATIC NECROSIS; RAINBOW-TROUT; BODY-WEIGHT; SEXUAL-MATURATION; GENOME; ARCHITECTURE; Salvelinus fontinalis; QUANTITATIVE TRAIT LOCI; SALMON SALMO-SALAR; POPULATIONS; [SDV]Life Sciences [q-bio]; Canada; Salmo salar
• Online Access: https://hal.science/hal-01251103; https://hal.science/hal-01251103/document; https://hal.science/hal-01251103/file/Sauvage,%20Vagner%20et%20al%202012b.pdf; https://doi.org/10.1534/g3.112.001990

International audience 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 ...