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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]

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Abstract: Quantitative trait loci (QTL) for age at smoltification and adult maturation have been mapped in several salmonid species but less is known about precocious male parr maturity. Phenotypic information on length at age, precocious male parr maturation (paedogenesis), early smoltification, and adult sexual maturation was recorded for four double-backcross families of F1 European/North American trans-Atlantic salmon that had been genotyped for 320 (family A) or 121 (families B, C and D) single nucleotide polymorphisms (SNPs). The locations of QTL for early smoltification and for precocious parr and adult maturation in Atlantic salmon (Salmo salar) were identified and then compared with QTL in homologous chromosomal arms of rainbow trout (Oncorhynchus mykiss). Novel QTL for precocious male parr maturation on Ssa05, Ssa07, Ssa09, Ssa10, Ssa12, Ssa16 and Ssa20 were significant at the genome-wide level as were QTL for early smolting detected on chromosomes Ssa05, Ssa08, Ssa13, and Ssa23. As predicted, precocious male parr were significantly less likely to become early smolts. Two QTL for adult sexual maturation on chromosomes Ssa21 and Ssa23 were significant at the chromosome-wide level as were QTL for adult length on Ssa05 and Ssa24. Separate analysis of family A resulted in novel QTL being detected on Ssa01q for early smolting, Ssa17 and Ssa22 for precocious maturation, and on Ssa03 and Ssa20 for length at the early smolt measuring period. The two chromosomes (Ssa21 and Ssa23) that contained QTL for adult maturation were homologous to two chromosomes (Omy22 and Omy4) that contain QTL for adult maturation in rainbow trout. [Copyright &y& Elsevier]