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Little is known about the genetic architecture of traits important for salmonid restoration ecology. We mapped quantitative trait loci (QTL) using single nucleotide polymorphisms (SNPs) for juvenile body length, weight, shape, and vertical skin pigmentation patterns (parr marks) within three hybrid backcross families between European and North American subspecies of Atlantic salmon. Amounts of variation in skin colour and pattern quantified in the two second-generation transAtlantic families exceeded the ranges seen in purebred populations. GridQTL analyses using low-density female-specific linkage maps detected QTL showing experiment-wide significance on Ssa02, Ssa03, Ssa09, Ssa11, Ssa19, and Ssa26/28 for both length and weight; on Ssa04 and Ssa23 for parr mark number; on Ssa09 and Ssa13 for parr mark contrast; and on Ssa05, Ssa07, Ssa10, Ssa11, Ssa18, Ssa23, and Ssa26/28 for geometric morphometric shape coordinates. Pleiotrophic QTL on Ssa11 affected length, weight, and shape. No QTL was found that explained more than 10% of the phenotypic variance in pigmentation or shape traits. Each QTL was approximately positioned on the physical map of the Atlantic salmon genome. Some QTL locations confirmed previous studies but many were new. Studies like ours may increase the success of salmon restoration projects by enabling better phenotypic and genetic matching between introduced and extirpated strains. Key words: conservation genetics, geometric morphometrics, parr marks, quantitative trait mapping, single nucleotide polymorphisms. Peu de choses sont connues au sujet de l'architecture genetique des caracteres importants en matiere de l'ecologie de retablissement chez les salmonides. Les auteurs ont effectue une cartographie QTL a l'aide de marqueurs mononucleotidiques (SNP) pour la taille, la masse, la forme et la pigmentation cutanee verticale (marques de tacon) chez les juveniles au sein de trois familles hybrides retrocroisees entre les sous-especes europeennes et nord-americaines du saumon atlantique. La variation pour la couleur et les motifs de la peau a ete quantifiee au sein des deux familles transatlantiques de seconde generation et elle excedait celle rencontree au sein des populations pures. Des analyses GridQTL a l'aide de cartes genetiques femelles a faible densite en marqueurs ont permis de detecter des QTL significatifs sur Ssa02, Ssa03, Ssa09, Ssa11, Ssa19 et Ssa26/28 tant pour la taille que pour la masse, sur Ssa04 et Ssa23 pour le nombre de marques de tacon, sur Ssa09 et Ssa13 pour le contraste des marques de tacon, et sur Ssa05, Ssa07, Ssa10, Ssa11, Ssa18, Ssa23 et Ssa26/28 pour les coordonnees morphometriques geometriques. Des QTL pleiotropiques sur Ssa11 affectaient la taille, la masse et la forme. Aucun QTL expliquant plus de 10 % de la variation phenotypique pour la pigmentation ou la taille n'a ete identifie. Chaque QTL a ete assigne a une position approximative sur la carte physique du genome du saumon atlantique. Certaines positions de QTL confirmaient celles rapportees dans des etudes precedentes, mais plusieurs etaient inedites. Des etudes comme celle-ci peuvent permettre d'accroitre le succes des projets de repeuplement en permettant une meilleure concordance phenotypique et genetique entre les individus introduits et extirpes. [Traduit par la Redaction] Mots-cles : genetique de la conservation, morphometrie geometrique, marques de tacon, cartographie de caracteres quantitatifs, polymorphisme mononucleotidique., Introduction Atlantic salmon (Salmo salar) is an economically important species, generating large revenues in the aquaculture industry, and in the recreational angling industry. There has been an overall decline of [...]

Infectious salmon anaemia (ISA) is a highly virulent viral disease of Atlantic salmon that causes massive economic losses to infected aquaculture operations. Our goal was to detect and map quantitative trait loci (QTL) that confer resistance to ISA in an admixed commercial strain of Atlantic salmon that was largely founded from the Saint John River (SJR) in North America. Full‐sibling families were challenged with a virulent strain of ISA virus. Mortality was tracked during two annual trials with individual fish that survived to the end of the trial being classified as 'resistant', and those that died were classified as 'susceptible'. Ten families with intermediate levels of mortality and an average size of 54.2 individuals were chosen for genotyping with a 50K SNP array designed for the SJR strain. Single nucleotide polymorphisms that were segregating within families were first used to make a composite 11K female linkage map that was then used to find the positions of QTL for ISA resistance using a half‐sib model. The dam‐based HS model detected a total of three QTL for ISA resistance including an experiment‐wide significant QTL on Ssa25 that accounted for 8.3% of the phenotypic variance and chromosome‐wide significant QTL on Ssa03 and on Ssa04 that accounted for 6.0% and 6.6% respectively. We conclude that classic linkage mapping within families continues to be an important method of detecting QTL for oligogenic traits in strains founded from multiple populations. Single nucleotide polymorphisms with moderate trait effects are being used to select within families for more ISA‐resistant strains of Atlantic salmon. [ABSTRACT FROM AUTHOR]

Abstract: Our objective was to detect single nucleotide polymorphisms (SNPs) associated with resistance to the salmon louse in the Saint John River aquacultural population of North American Atlantic salmon using estimated breeding values (EBVs) and 6K genotypes from the parent‐generation and lice count phenotypes from the challenged, but ungenotyped, offspring‐generation. In 2011 and 2012, we challenged recent smolts with approximately 100 copepodids each. Fish were euthanized once the lice reached the chalimus stages and lice count, sex, tank and salt water weight were recorded. We used a multiple trait model to estimate breeding values for the parent‐generation using their own fresh water weights and the salt water weights and lice counts of the offspring‐generation. Salmon lice count heritability for untransformed and transformed data was 0.17 and 0.29 respectively. Two different genome‐wide association study methods were compared: (i) forward multiple linear regression and (ii) a mixed linear model using principal components to correct for population stratification as implemented in the egscore function of GenABEL. The two methods detected different SNPs located on different chromosomes. The multiple regression method incorporated 70 SNPs found on chromosomes 2, 7, 9, 12, 14, 15, 21, 22, 1p/23, 24. Many SNPs entered into the forward multiple regression are likely to be false positives from not correcting for the observed population stratification and cryptic relatedness. In contrast, the mixed linear model identified only two SNPs, one on chromosome 1p/23 (6.9%) and one on chromosome 1q (6.1%) consistent with louse‐resistance being a quantitative trait. [ABSTRACT FROM AUTHOR]