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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.

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]