The life history of anadromous salmonids entails movements between freshwater and seawater environments. To cope with the physiological demands associated with such behaviour, salmonids and other teleosts have evolved the capacity to change their ionoregulatory condition by altering states of ion uptake (hyper-osmoregulation) and excretion (hypo-osmoregulation). In teleosts, mitochondria-rich cells are located in the epithelial layer of fish gill tissue and play a major role in hypo-osmoregulation. The molecular mechanisms within and around mitochondria-rich cells function together to facilitate the removal of Na+ and Cl- from blood plasma and are an integral part of the mitochondria-rich cell model
. Active exchange of cytoplasmic Na+ with intercellular K+ by Na+/K+-ATPase pumps maintains an electrochemical gradient sufficient to move intercellular Cl- across the basolateral membrane and into the cell via Na+/K+/2Cl- (NKCC) cotransporters. Cl- exits the cell across the apical membrane through embedded cystic fibrosis transmembrane conductance regulator-like anion channels (CFTR). Intercellular Na+ is secreted through leaky cation-selective paracellular pores between accessory cells and mitochondria-rich cells
[1, 2], where variation in permeability rates are thought to be a function of claudin isoform type
Several genes that are not part of the current mitochondria-rich cell model are also involved in the hypo-osmoregulatory process. Insulin-like growth factor 2 (IGF2) transcription is positively correlated with elevated salinity tolerance
. Growth hormone (GH) levels
 also regulate this balance, as illustrated by GH injections that correlate with a rapid increase in salinity tolerance capacity
. Such short-term effects could be related to changes in gill tissue cell structure, as GH has been connected with seawater-induced mitochondria-rich cell hyperplasia and hypertrophy
[8, 9]. Moreover, Atlantic salmon smolts (i.e., fish prepared for seawater) have larger relative gill weights compared to non-smolts (i.e., fish prepared for freshwater) of equal size
, which suggests that smoltification-induced changes in cell structure may be reflected by changes in gill weight. The localization of salinity tolerance QTL in multiple species to linkage groups where GH (i.e., on RT-9q & AC-20) and IGF2 are mapped (i.e., on RT-27 & AC-4/19)
[11–15] is consistent with the hypothesis that allelic variation at the loci encoding these hormones exerts significant affects on hypo-osmoregulatory capacity. Unsurprisingly, growth hormone receptor (GHR), which modulates tissue-specific activity of GH
, is upregulated concurrently with elevated salinity and the onset of smoltification in rainbow trout and Atlantic salmon, respectively
[17, 18]. Collagen type I alpha I (COL1A1), secreted protein acidic and rich in cysteine (SPARC)
, and calcium-sensing receptors (CaSR)
 are also upregulated in Atlantic salmon smolts. COL1A1 appears to be involved in the composition of the extracellular matrix and arch formation of fish gills
, while SPARC has been associated with tissue remodelling. By binding to structural proteins such as collagen type I, SPARC regulates cellular interactions with the extracellular matrix
. Lastly, calcium-sensing receptors (CaSR) are thought to act as osmosensors by sending regulatory signals in response to elevated plasma ion concentrations
Within the Salmonidae family there is wide variation in both anadromy and salinity tolerance capacity among species
[22–27]. Sea-run Atlantic salmon (Salmo salar) are iteroparous and have high saltwater tolerance, spending multiple years at sea between river spawning migrations. At the other extreme, anadromy in Arctic charr (Salvelinus alpinus) involves shorter periods of seawater residency (i.e., a few months), which is accompanied by a relatively low capacity for hypo-osmoregulation
[9, 26, 28]. Both of these species also show wide intraspecific variation in salinity tolerance capacity.
While in seawater, different Atlantic salmon families show large differences in blood plasma osmolality concentrations
, while wide disparity in seawater-induced mortality
 has been observed in different strains of Arctic charr, as have family-based differences in Na+/K+-ATPase activity levels and blood plasma osmolality concentrations
. Such studies suggest that inter- and intraspecific variation in salinity tolerance capacity is affected by genetic variation. In fact, recent research shows that quantitative trait loci (QTL) for various salinity tolerance performance indicator traits localize to homologous linkage groups in rainbow trout
 and Arctic charr
. These QTL localize to linkage groups that are predicted to contain genes for the primary mechanisms from the mitochondria-rich cell model (e.g., ATP1α1b, NKCC, and CFTR)
The extent that the genetic basis of salinity tolerance is conserved across Salmonidae species is unclear. Well established chromosome homologies among Arctic charr and rainbow trout
[30, 31] have facilitated assessments of the conservation of salinity tolerance QTL. Several tentative QTL homologies have been identified, but differences in experimental design and genetic map resolution have made comparisons difficult. Assessment of the salinity tolerance QTL positions in Atlantic salmon would contribute knowledge on the conserved homologous QTL genomic locations influencing this trait in salmonids.
The evolutionary lineage of modern salmonids is unique in that it is punctuated by four whole-genome duplication events. Two whole-genome duplication events have occurred in all vertebrate lineages (i.e., 1R, 2R)
. Doubly conserved synteny blocks among Tetraodon nigroviridis and Homo sapiens show that a third whole-genome duplication occurred in fishes (i.e., 3R). In modern salmonids, residual tetrasomic inheritance, multivalent formations, and Hox gene duplication patterns suggest that a fourth whole-genome duplication occurred in the salmonid ancestor some 25-100 million years ago (i.e., 4R)
[34–36]. Evidence suggests that the 4R duplication may have had ramifications for the evolution of salinity tolerance, for in Arctic charr there are multiple instances where trait-specific QTL localize to homeologous linkage groups (e.g., predicted duplicates ATP1α1b loci overlap with QTL detected on AC-12 and -27)
[15, 30, 37, 38]. Such patterns would be expected if duplicated loci were subfunctionalized or if a redundant locus was neofunctionalized, contrary to the usual fate of duplicated loci (pseudogenization)
. In addition, duplicate gene function may simply be retained because of positive selective advantage. On the other hand, patterns suggestive of QTL homeology would be indistinguishable from patterns resulting from QTL linked to non-paralogous loci, if such loci were tightly linked in the salmonid ancestor prior to the 4R duplication event and have since been conserved on only reciprocal homeologues in extant salmonids (see doubly conserved synteny blocks in
). Interestingly, the latter scenario is consistent with observations that suggest some salinity tolerance candidate genes occur in clusters within the same linkage group region
, and could singly or in combination contribute to the apparent conserved QTL homeologies that were identified.
Disparity in genomic structure among Atlantic salmon (2n = 54-58; NF = 72–74), Arctic charr (2n = 78; NF = 100) and rainbow trout (2n = 58-64; NF = 100-104)
[40, 41] could have lead to differences in the arrangement of genes related to salinity tolerance. The non-randomness of gene order
 in conjunction with the co-expression of gene clusters in eukaryotes
 implies that gene arrangement is important in the evolution of phenotypes. More specifically, it suggests that genes in close proximity are more likely to be involved in the same biochemical pathway
, and that disruptions in these regions could conceivably affect development of the respective phenotype. The availability of the reconstructed 2R proto-Actinopterygian ancestral karyotype and the sequenced genomes of multiple 3R teleost species provide an opportunity to examine the extent that genomic rearrangements may have affected the relative positions of salinity tolerance candidate genes in 3R and 4R genomes. The approximate positions of candidate genes in 4R genomes can be predicted using knowledge of their precise positions in 3R genomes in conjunction with synteny patterns evident among 3R and 4R species. Comparisons with the positions of salinity tolerance QTL would then provide an opportunity to assess whether disparity in salinity tolerance capacity could be correlated with differences in genomic structure.
The characterization of salinity tolerance QTL in Atlantic salmon and subsequent comparisons with Arctic charr and rainbow trout will allow us to determine which QTL are conserved across species using information from three different genera (Salmo, Salvelinus, and Oncorhynchus). Comparative genomics approaches will also allow us to infer if genomic rearrangements have affected the relative positions of salinity tolerance candidate genes in the genomes of salmonids. Using two out-bred Atlantic salmon families, we examined the genetic architecture of salinity tolerance performance traits after exposure to seawater in a controlled environment designed to simulate natural conditions. We addressed the following questions: (1) Does genetic variation have a significant effect on salinity tolerance performance traits in Atlantic salmon? (2) Do salinity tolerance QTL share homeologous affinities? (3) Do QTL share homologous affinities with QTL in other salmonids? (4) Do QTL localize to linkage groups that contain or are predicted to contain candidate genes? (5) Is the relative arrangement of candidate genes different among 2R, 3R, and 4R species? (6) Is disparity in salinity tolerance capacity among salmonid species correlated with variation in genomic structure?