Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs

The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (>50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydrostatic pressure, low temperature, and low light, but the genomic mechanisms underlying evolution in these environments are rarely known. Here, we compare genomic divergence between a deep-water morph adapted to depths of up to 288 m and a larger, piscivorous pelagic morph occupying shallower depths. Using both a SNP array and resequencing of whole nuclear and mitochondrial genomes, we find clear genetic divergence (F_ST  = 0.11-0.15) between deep and shallow water morphs, despite an absence of morph divergence across the mitochondrial genome. Outlier analyses identified many diverged genomic regions containing genes enriched for processes such as gene expression and DNA repair, cardiac function, and membrane transport. Detection of putative copy number variants (CNVs) uncovered 385 genes with CNVs distinct to piscivorous morphs, and 275 genes with CNVs distinct to deep-water morphs, enriched for processes associated with synapse assembly. Demographic analyses identified evidence for recent and local morph divergence, and ongoing reductions in diversity consistent with postglacial colonization. Together, these results show that Arctic Charr morph divergence has occurred through genome-wide differentiation and elevated divergence of genes underlying multiple cellular and physiological processes, providing insight into the genomic basis of adaptation in a deep-water habitat following postglacial recolonization.

The interaction of resource use and gene flow on the phenotypic divergence of benthic and pelagic morphs of Icelandic Arctic charr (Salvelinus alpinus)

Conceptual models of adaptive divergence and ecological speciation in sympatry predict differential resource use, phenotype-environment correlations, and reduced gene flow among diverging phenotypes. While these predictions have been assessed in past studies, connections among them have rarely been assessed collectively. We examined relationships among phenotypic, ecological, and genetic variation in Arctic charr (Salvelinus alpinus) from six Icelandic localities that have undergone varying degrees of divergence into sympatric benthic and pelagic morphs. We characterized morphological variation with geometric morphometrics, tested for differential resource use between morphs using stable isotopes, and inferred the amount of gene flow from single nucleotide polymorphisms. Analysis of stable isotopic signatures indicated that sympatric morphs showed similar difference in resource use across populations, likely arising from the common utilization of niche space within each population. Carbon isotopic signature was also a significant predictor of individual variation in body shape and size, suggesting that variation in benthic and pelagic resource use is associated with phenotypic variation. The estimated percentage of hybrids between sympatric morphs varied across populations (from 0% to 15.6%) but the majority of fish had genotypes (ancestry coefficients) characteristic of pure morphs. Despite evidence of reduced gene flow between sympatric morphs, we did not detect the expected negative relationship between divergence in resource use and gene flow. Three lakes showed the expected pattern, but morphs in the fourth showed no detectable hybridization and had relatively low differences in resource use between them. This coupled with the finding that resource use and genetic differentiation had differential effects on body shape variation across populations suggests that reproductive isolation maintains phenotypic divergence between benthic and pelagic morphs when the effects of resource use are relatively low. Our ability to assess relationships between phenotype, ecology, and genetics deepens our understanding of the processes underlying adaptive divergence in sympatry.

Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish

The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such, quantifying diversity is central to combating ongoing widespread reductions in biodiversity. With the advent of next-generation sequencing, several methods now exist for resolving fine-scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here, we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP) array to resolve fine-scale population structure in a critically important salmonid in north eastern Canada, Arctic Charr (Salvelinus alpinus). We also assess the utility of sequenced microsatellites for fisheries applications by quantifying the spatial scales of movement and exploitation through genetic assignment of fishery samples to rivers of origin and comparing these results with a 29-year tagging dataset. Self-assignment and simulation-based analyses of 111 genome-wide microsatellite loci and 500 informative SNPs from 28 populations of Arctic Charr in north-eastern Canada identified largely river-specific genetic structure. Despite large differences (~4X) in the number of loci surveyed between panels, mean self-assignment accuracy was similar with the microsatellite loci and the SNP panel (>90%). Subsequent analysis of 996 fishery-collected samples using the microsatellite panel revealed that larger rivers contribute greater numbers of individuals to the fishery and that coastal fisheries largely exploit individuals originating from nearby rivers, corroborating results from traditional tagging experiments. Our results demonstrate the efficacy of sequence-based microsatellite genotyping to advance understanding of fine-scale population structure and harvest composition in northern and understudied species.

A way forward with eco evo devo: an extended theory of resource polymorphism with postglacial fishes as model systems

A major goal of evolutionary science is to understand how biological diversity is generated and altered. Despite considerable advances, we still have limited insight into how phenotypic variation arises and is sorted by natural selection. Here we argue that an integrated view, which merges ecology, evolution and developmental biology (eco evo devo) on an equal footing, is needed to understand the multifaceted role of the environment in simultaneously determining the development of the phenotype and the nature of the selective environment, and how organisms in turn affect the environment through eco evo and eco devo feedbacks. To illustrate the usefulness of an integrated eco evo devo perspective, we connect it with the theory of resource polymorphism (i.e. the phenotypic and genetic diversification that occurs in response to variation in available resources). In so doing, we highlight fishes from recently glaciated freshwater systems as exceptionally well-suited model systems for testing predictions of an eco evo devo framework in studies of diversification. Studies on these fishes show that intraspecific diversity can evolve rapidly, and that this process is jointly facilitated by (i) the availability of diverse environments promoting divergent natural selection; (ii) dynamic developmental processes sensitive to environmental and genetic signals; and (iii) eco evo and eco devo feedbacks influencing the selective and developmental environments of the phenotype. We highlight empirical examples and present a conceptual model for the generation of resource polymorphism - emphasizing eco evo devo, and identify current gaps in knowledge.

Natural selection for body shape in resource polymorphic Icelandic Arctic charr

Resource polymorphisms exhibit remarkable intraspecific diversity and in many cases are expected to be maintained by diversifying selection. Phenotypic trade-offs can constrain morphologically intermediate individuals from effectively exploiting both alternate resources, resulting in ecological barriers to gene flow. Determining if and how phenotypic trade-offs cause fitness variation in the wild is challenging because of phenotypic and environmental correlations associated with alternative resource strategies. We investigated multiple pathways through which morphology could affect organismal performance, as measured by growth rate, and whether these effects generate diversifying selection in polymorphic Icelandic Arctic charr (Salvelinus alpinus) populations. We considered direct effects of morphology on growth and indirect effects via trophic resource use, estimated by stable isotopic signatures, and via parasitism associated with trophic resources. We sampled over 3 years in (lakes) Thingvallavatn and Vatnshlíðarvatn using the extended selection gradient path analytical approach and estimating size-dependent mortality. We found evidence for diversifying selection only in Thingvallavatn: more streamlined and terminally mouthed planktivore charr experienced greater growth, with the opposite pattern in small benthic charr. However, this effect was mediated by parasitism and nontrophic pathways, rather than trophic performance as often expected. Detection of between-morph differences in the presence (Vatnshlíðarvatn) and direction (Thingvallavatn) of size-dependent mortality, together with nontrophic effects of shape, suggests that a morphological trophic performance explanation for polymorphism is insufficient. This rare insight into selection during early diversification suggests that a complex of interacting local factors must be considered to understand how phenotype influences fitness, despite morphological variation reflecting intuitive trade-off explanations.

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly

Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes.

Oral Complaints Related to Climacteric Symptoms in Oöphorectomized Women

Numerous oral complaints have been attributed to the female climacteric including altered taste, a burning sensation and xerostomia. However, the data relating these symptoms to the climacteric require elucidation as there have been no adequately controlled studies. In the present investigation, a group of 145 oöphorectomized women were followed for one year. Approximately half were treated with oestrogen replacement and the remainder with a placebo. The results indicate that the hormone had no direct effect upon the oral symptoms but that there was a general increase in somatic complaints which appeared to be related to the degree of neurosis experienced. This is turn can be attributed to vasomotor changes which are under the control of oestrogen.

Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout

We tested whether genes differentially expressed between large and small rainbow trout co-localized with familial QTL regions for body size. Eleven chromosomes, known from previous work to house QTL for weight and length in rainbow trout, were examined for QTL in half-sibling families produced in September (1 XY male and 1 XX neomale) and December (1 XY male). In previous studies, we identified 108 candidate genes for growth expressed in the liver and white muscle in a subset of the fish used in this study. These gene sequences were BLASTN aligned against the rainbow trout and stickleback genomes to determine their location (rainbow trout) and inferred location based on synteny with the stickleback genome. Across the progeny of all three males used in the study, 63.9% of the genes with differential expression appear to co-localize with the QTL regions on 6 of the 11 chromosomes tested in these males. Genes that co-localized with QTL in the mixed-sex offspring of the two XY males primarily showed up-regulation in the muscle of large fish and were related to muscle growth, metabolism, and the stress response.

Comparison of growth-related traits and gene expression profiles between the offspring of neomale (XX) and normal male (XY) rainbow trout

All-female lines of fish are created by crossing sex reversed (XX genotype) males with normal females. All-female lines avoid the deleterious phenotypic effects that are typical of precocious maturation in males. To determine whether all-female and mixed sex populations of rainbow trout (Oncorhynchus mykiss) differ in performance, we compared the growth and gene expression profiles in progeny groups produced by crossing a XX male and a XY male to the same five females. Body weight and length were measured in the resulting all-female (XX) and mixed sex (XX/XY) offspring groups. Microarray experiments with liver and white muscle were used to determine if the gene expression profiles of large and small XX offspring differ from those in large and small XX/XY offspring. We detected no significant differences in body length and weight between offspring groups but XX offspring were significantly less variable in the value of these traits. A large number of upregulated genes were shared between the large XX and large XX/XY offspring; the small XX and small XX/XY offspring also shared similar expression profiles. No GO category differences were seen in the liver or between the large XX and large XX/XY offspring in the muscle. The greatest differences between the small XX and small XX/XY offspring were in the genes assigned to the "small molecule metabolic process" and "cellular metabolic process" GO level 3 categories. Similarly, genes within these categories as well as the category "macromolecule metabolic process" were more highly expressed in small compared to large XX fish.

Phenotypic and QTL allelic associations among embryonic developmental rate, body size, and precocious maturation in male rainbow trout

We examined associations among embryonic developmental rate (EDR) as measured by hatching time, juvenile body weight (BW) and propensity for precocial sexual maturation (PM) at two years in two sets of diallel crosses of rainbow trout produced in two spawning seasons (September and December) at both the phenotypic and genotypic levels. Dams and sires had highly significant effects on the body weight of their male juvenile progeny on three measurement dates where parental effects remained consistent through time. Dams spawning earlier in the season produced a greater number of mature male progeny (56.7%) than did later spawning females (25.6%). The families from the December lot showed the expected associations among traits in that earlier hatching fish were significantly heavier on all three measurement dates than later hatching fish and were more likely to mature earlier when families were combined. Moreover, earlier maturing fish were significantly heavier on the third measurement date than those that did not mature. In the September lot, mature fish were significantly heavier as juveniles on all three measurement dates than immature fish as predicted but no significant associations were detected between EDR and BW or between PM and EDR. Significant QTL were detected for all three traits but the linkage group location varied depending on the trait and half-sib group analyzed (across dams and sires in each lot). A strong QTL for EDR with genome-wide effects was detected on linkage group RT-8 in all four half-sib analyses. None of the four linkage groups analyzed had QTL for all three traits. However, the phenotypic association between EDR and BW observed in the December lot was supported by the co-localization of QTL to linkage group RT-8 and a positive coupling of allelic effects. RT-8 marker alleles significantly associated with faster EDR were also associated with larger BW and this was observed in numerous families on all three measurement dates. Linkage group RT-24 had weaker QTL for all three traits in the September lot but these were not detected in the same half-sib group simultaneously. At the allelic level, marker alleles for faster EDR were also associated with BW but only at the third measurement date and the progeny of one male. Similarly, RT-30 had weaker QTL for EDR and PM in the December paternal half-sib analysis but no associations were evident at the allelic level. The detection of associations between life history traits and growth at both the phenotypic and genotypic levels has significant implications to aquaculture breeding programs where selection for a desirable trait may lead to unwanted alterations of other traits. Furthermore, the differences between spawning season lots emphasize the complex interaction between environment and genotype on economically important traits and the resulting challenges for aquaculture.

Hidden genetic variation evolves with ecological specialization: the genetic basis of phenotypic plasticity in Arctic charr ecomorphs

The genetic variance that determines phenotypic variation can change across environments through developmental plasticity and in turn play a strong role in evolution. Induced changes in genotype-phenotype relationships should strongly influence adaptation by exposing different sets of heritable variation to selection under some conditions, while also hiding variation. Therefore, the heritable variation exposed or hidden from selection is likely to differ among habitats. We used ecomorphs from two divergent populations of Arctic charr (Salvelinus alpinus) to test the prediction that genotype-phenotype relationships would change in relation to environment. If present over several generations this should lead to divergence in genotype-phenotype relationships under common conditions, and to changes in the amount and type of hidden genetic variance that can evolve. We performed a common garden experiment whereby two ecomorphs from each of two Icelandic lakes were reared under conditions that mimicked benthic and limnetic prey to induce responses in craniofacial traits. Using microsatellite based genetic maps, we subsequently detected QTL related to these craniofacial traits. We found substantial changes in the number and type of QTL between diet treatments and evidence that novel diet treatments can in some cases provide a higher number of QTL. These findings suggest that selection on phenotypic variation, which is both genetically and environmentally determined, has shaped the genetic architecture of adaptive divergence in Arctic charr. However, while adaptive changes are occurring in the genome there also appears to be an accumulation of hidden genetic variation for loci not expressed in the contemporary environment.

Molecular markers for variation in spawning date in a hatchery population of rainbow trout (Oncorhynchus mykiss)

We examined the distribution of alleles at 63 microsatellite loci distributed across 29 linkage groups in broodstock females from a commercial population of rainbow trout spawning on different dates throughout the season (August to January). A total of 368 females, 184 and 117 females from each of the tail-ends of the spawning distribution and a subsample of 67 females spawning in the middle, were used to detect marker-trait associations. Twenty-one loci in a subset of genomic regions (RT-5, 7, 8, 10, 12, 14, 15, 22, 23, 24, 25, 29, 30, and 31) were significantly associated with variation in spawning date. Many of these markers localize to regions with known spawning date quantitative trait loci based on previous studies. An individual assignment analysis was used to test how well the molecular data could be used to assign individuals to their correct spawning group, and markers were given a ranking reflecting their contribution to the accuracy of assignment. The top 15 ranked markers were successful at assigning the majority of females to the correct spawning group based on genotype with an average accuracy of 76 %. The most likely genes that could contribute to these differences in spawning date are discussed. Together, these data indicate that the loci could be incorporated into a selection index with phenotype data to increase the accuracy of selection for spawning date.

Differential gene expression in small and large rainbow trout derived from two seasonal spawning groups

Background

Growth in fishes is regulated via many environmental and physiological factors and is shaped by the genetic background of each individual. Previous microarray studies of salmonid growth have examined fish experiencing either muscle wastage or accelerated growth patterns following refeeding, or the influence of growth hormone and transgenesis. This study determines the gene expression profiles of genetically unmanipulated large and small fish from a domesticated salmonid strain reared on a typical feeding regime. Gene expression profiles of white muscle and liver from rainbow trout (Oncorhynchus mykiss) from two seasonal spawning groups (September and December lots) within a single strain were examined when the fish were 15 months of age to assess the influence of season (late fall vs. onset of spring) and body size (large vs. small).

Results

Although IGFBP1 gene expression was up-regulated in the livers of small fish in both seasonal lots, few expression differences were detected in the liver overall. Faster growing Dec. fish showed a greater number of differences in white muscle expression compared to Sept. fish. Significant differences in the GO Generic Level 3 categories ‘response to external stimulus’, ‘establishment of localization’, and ‘response to stress’ were detected in white muscle tissue between large and small fish. Larger fish showed up-regulation of cytoskeletal component genes while many genes related to myofibril components of muscle tissue were up-regulated in small fish. Most of the genes up-regulated in large fish within the ‘response to stress’ category are involved in immunity while in small fish most of these gene functions are related to apoptosis.

Conclusions

A higher proportion of genes in white muscle compared to liver showed similar patterns of up- or down-regulation within the same size class across seasons supporting their utility as biomarkers for growth in rainbow trout. Differences between large and small Sept. fish in the ‘response to stress’ and ‘response to external stimulus’ categories for white muscle tissue, suggests that smaller fish have a greater inability to handle stress compared to the large fish. Sampling season had a significant impact on the expression of genes related to the growth process in rainbow trout.

An integrated transcriptomic and comparative genomic analysis of differential gene expression in Arctic charr (Salvelinus alpinus) following seawater exposure

High-throughput RNA sequencing was employed to compare expression profiles in two Arctic charr (Salvelinus alpinus) families post seawater exposure to identify genes and biological processes involved in hypo-osmoregulation and regulation of salinity tolerance. To further understand the genetic architecture of hypo-osmoregulation, the genomic organization of differentially expressed (DE) genes was also analysed. Using a de novo gill transcriptome assembly we found over 2300 contigs to be DE. Major transporters from the seawater mitochondrion-rich cell (MRC) complex were up-regulated in seawater. Expression ratios for 257 differentially expressed contigs were highly correlated between families, suggesting they are strictly regulated. Based on expression profiles and known molecular pathways we inferred that seawater exposure induced changes in methylation states and elevated peroxynitrite formation in gill. We hypothesized that concomitance between DE immune genes and the transition to a hypo-osmoregulatory state could be related to Cl- sequestration by antimicrobial defence mechanisms. Gene Ontology analysis revealed that cell division genes were up-regulated, which could reflect the proliferation of ATP1α1b-type seawater MRCs. Comparative genomics analyses suggest that hypo-osmoregulation is influenced by the relative proximities among a contingent of genes on Arctic charr linkage groups AC-4 and AC-12 that exhibit homologous affinities with a region on stickleback chromosome Ga-I. This supports the hypothesis that relative gene location along a chromosome is a property of the genetic architecture of hypo-osmoregulation. Evidence of non-random structure between hypo-osmoregulation candidate genes was found on AC-1/11 and AC-28, suggesting that interchromosomal rearrangements played a role in the evolution of hypo-osmoregulation in Arctic charr.

Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes

Osmoregulatory capabilities have played an important role in the evolution, dispersal, and diversification of vertebrates. To better understand the genetic architecture of hypo-osmoregulation in fishes and to determine which genes and biological processes affect intraspecific variation in salinity tolerance, we used mRNA sequence libraries from Arctic charr gill tissue to compare gene expression profiles in fish exhibiting divergent salinity tolerance quantitative trait locus (QTL) genotypes. We compared differentially expressed genes with QTL positions to gain insight about the nature of the underlying polymorphisms and examined gene expression within the context of genome organization to gain insight about the evolution of hypo-osmoregulation in fishes. mRNA sequencing of 18 gill tissue libraries produced 417 million reads, and the final reduced de novo transcriptome assembly consisted of 92,543 contigs. Families contained a similar number of differentially expressed contigs between high and low salinity tolerance capacity groups, and log2 expression ratios ranged from 10.4 to -8.6. We found that intraspecific variation in salinity tolerance capacity correlated with differential expression of immune response genes. Some differentially expressed genes formed clusters along linkage groups. Most clusters comprised gene pairs, though clusters of three, four, and eight genes were also observed. We postulated that conserved synteny of gene clusters on multiple ancestral and teleost chromosomes may have been preserved via purifying selection. Colocalization of QTL with differentially expressed genes suggests that polymorphisms in cis-regulatory elements are part of a majority of QTL.

Comparative analysis of genetic parameters and quantitative trait loci for growth traits in Fraser strain Arctic charr (Salvelinus alpinus) reared in freshwater and brackish water environments

To determine the potential for genetic improvement in Fraser strain Arctic charr (AC, Salvelinus alpinus), we calculated genetic parameters for BW and condition factor (K) and tested if previously identified QTL for these traits were detectable across a commercial broodstock reared in both freshwater (FRW) and brackish water (BRW). Individuals from 30 full-sib families were reared up to 29 mo of age in FRW and BRW tanks at a commercial facility. Heritability for BW and K was moderate in FRW (0.29 to 0.38) but lower in BRW (0.14 to 0.17). Genetic correlations for BW across environments were positive and moderate (0.33 to 0.67); however, equivalent K correlations were very weak (0.24 to 0.37). We identified a single BW QTL with experimentwide effects on linkage group AC-8, 4 BW QTL (AC-4, -13, -14, and -19), and 3 K QTL (AC-4, -5, and -20) with chromosomewide effects across families. Notably, the QTL on AC-8 had significant effects with BW at 3 out of 4 sampling dates in FRW and had significant allelic phase disequilibrium with BW across families, suggesting a tight coupling of the marker region to the QTL in this population. Body weight QTL were identified on AC-4 in both FRW and BRW environments and AC-4 was the only linkage group with a detectable QTL for both K and BW. Modest consistency of some QTL effects as well as moderate heritability in both environments suggests that there is some potential for genetic improvement of growth in this species even though gene × environment interactions are high.

Genomic arrangement of salinity tolerance QTLs in salmonids: a comparative analysis of Atlantic salmon (Salmo salar) with Arctic charr (Salvelinus alpinus) and rainbow trout (Oncorhynchus mykiss)

Background

Quantitative trait locus (QTL) studies show that variation in salinity tolerance in Arctic charr and rainbow trout has a genetic basis, even though both these species have low to moderate salinity tolerance capacities. QTL were observed to localize to homologous linkage group segments within putative chromosomal regions possessing multiple candidate genes. We compared salinity tolerance QTL in rainbow trout and Arctic charr to those detected in a higher salinity tolerant species, Atlantic salmon. The highly derived karyotype of Atlantic salmon allows for the assessment of whether disparity in salinity tolerance in salmonids is associated with differences in genetic architecture. To facilitate these comparisons, we examined the genomic synteny patterns of key candidate genes in the other model teleost fishes that have experienced three whole-genome duplication (3R) events which preceded a fourth (4R) whole genome duplication event common to all salmonid species.

Results

Nine linkage groups contained chromosome-wide significant QTL (AS-2, -4p, -4q, -5, -9, -12p, -12q, -14q -17q, -22, and −23), while a single genome-wide significant QTL was located on AS-4q. Salmonid genomes shared the greatest marker homology with the genome of three-spined stickleback. All linkage group arms in Atlantic salmon were syntenic with at least one stickleback chromosome, while 18 arms had multiple affinities. Arm fusions in Atlantic salmon were often between multiple regions bearing salinity tolerance QTL. Nine linkage groups in Arctic charr and six linkage group arms in rainbow trout currently have no synteny alignments with stickleback chromosomes, while eight rainbow trout linkage group arms were syntenic with multiple stickleback chromosomes. Rearrangements in the stickleback lineage involving fusions of ancestral arm segments could account for the 21 chromosome pairs observed in the stickleback karyotype.

Conclusions

Salinity tolerance in salmonids from three genera is to some extent controlled by the same loci. Synteny between QTL in salmonids and candidate genes in stickleback suggests genetic variation at candidate gene loci could affect salinity tolerance in all three salmonids investigated. Candidate genes often occur in pairs on chromosomes, and synteny patterns indicate these pairs are generally conserved in 2R, 3R, and 4R genomes. Synteny maps also suggest that the Atlantic salmon genome contains three larger syntenic combinations of candidate genes that are not evident in any of the other 2R, 3R, or 4R genomes examined. These larger synteny tracts appear to have resulted from ancestral arm fusions that occurred in the Atlantic salmon ancestor. We hypothesize that the superior hypo-osmoregulatory efficiency that is characteristic of Atlantic salmon may be related to these clusters.

Contemporary and historical evolutionary processes interact to shape patterns of within-lake phenotypic divergences in polyphenic pumpkinseed sunfish, Lepomis gibbosus

Historical and contemporary evolutionary processes can both contribute to patterns of phenotypic variation among populations of a species. Recent studies are revealing how interactions between historical and contemporary processes better explain observed patterns of phenotypic divergence than either process alone. Here, we investigate the roles of evolutionary history and adaptation to current environmental conditions in structuring phenotypic variation among polyphenic populations of sunfish inhabiting 12 postglacial lakes in eastern North America. The pumpkinseed sunfish polyphenism includes sympatric ecomorphs specialized for littoral or pelagic lake habitats. First, we use population genetic methods to test the evolutionary independence of within-lake phenotypic divergences of ecomorphs and to describe patterns of genetic structure among lake populations that clustered into three geographical groupings. We then used multivariate analysis of covariance (MANCOVA) to partition body shape variation (quantified with geometric morphometrics) among the effects of evolutionary history (reflecting phenotypic variation among genetic clusters), the shared phenotypic response of all populations to alternate habitats within lakes (reflecting adaptation to contemporary conditions), and unique phenotypic responses to habitats within lakes nested within genetic clusters. All effects had a significant influence on body form, but the effects of history and the interaction between history and contemporary habitat were larger than contemporary processes in structuring phenotypic variation. This highlights how divergence can be better understood against a known backdrop of evolutionary history.

Sex chromosome polymorphisms in Arctic charr and their evolutionary origins

Current data on the Y-specific sex-determining region of salmonid fishes from genera Salvelinus, Salmo, and Oncorhynchus indicate variable polymorphisms in the homologous chromosomal locations of the sex-specific determining region. In the majority of the Atlantic lineage Arctic charr, including populations from the Fraser River, in Labrador Canada, as well as Swedish and Norwegian strains, the sex-determining locus maps to linkage group AC-4. Previously, sex-linked polymorphisms (i.e., variation in the associated sex-linked markers on AC-4) have been described in Arctic charr. Here, we report further evidence for intraspecific sex linkage group polymorphisms in Arctic charr (i.e., the detection of the SEX locus on either the AC-1 or AC-21 linkage group) and a possible conservation of a sex linkage arrangement in Icelandic Arctic charr and Atlantic salmon, involving sex-linked markers on the AC-1/21 homeologs and the European AS-1/6 homeologous linkage groups in Atlantic salmon. The evolutionary origins for the multiple sex-determining regions within the salmonid family are discussed. We also relate the variable sex-determining regions in salmonids to their ancestral proto-teleost karyotypic origins and compare these findings with what has been observed in other teleost species in general.

The genetic basis of salinity tolerance traits in Arctic charr (Salvelinus alpinus)

BACKGROUND

The capacity to maintain internal ion homeostasis amidst changing conditions is particularly important for teleost fishes whose reproductive cycle is dependent upon movement from freshwater to seawater. Although the physiology of seawater osmoregulation in mitochondria-rich cells of fish gill epithelium is well understood, less is known about the underlying causes of inter- and intraspecific variation in salinity tolerance. We used a genome-scan approach in Arctic charr (Salvelinus alpinus) to map quantitative trait loci (QTL) correlated with variation in four salinity tolerance performance traits and six body size traits. Comparative genomics approaches allowed us to infer whether allelic variation at candidate gene loci (e.g., ATP1α1b, NKCC1, CFTR, and cldn10e) could have underlain observed variation.

RESULTS

Combined parental analyses yielded genome-wide significant QTL on linkage groups 8, 14 and 20 for salinity tolerance performance traits, and on 1, 19, 20 and 28 for body size traits. Several QTL exhibited chromosome-wide significance. Among the salinity tolerance performance QTL, trait co-localizations occurred on chromosomes 1, 4, 7, 18 and 20, while the greatest experimental variation was explained by QTL on chromosomes 20 (19.9%), 19 (14.2%), 4 (14.1%) and 12 (13.1%). Several QTL localized to linkage groups exhibiting homeologous affinities, and multiple QTL mapped to regions homologous with the positions of candidate gene loci in other teleosts. There was no gene × environment interaction among body size QTL and ambient salinity.

CONCLUSIONS

Variation in salinity tolerance capacity can be mapped to a subset of Arctic charr genomic regions that significantly influence performance in a seawater environment. The detection of QTL on linkage group 12 was consistent with the hypothesis that variation in salinity tolerance may be affected by allelic variation at the ATP1α1b locus. IGF2 may also affect salinity tolerance capacity as suggested by a genome-wide QTL on linkage group 19. The detection of salinity tolerance QTL in homeologous regions suggests that candidate loci duplicated from the salmonid-specific whole-genome duplication may have retained their function on both sets of homeologous chromosomes. Homologous affinities suggest that loci affecting salinity tolerance in Arctic charr may coincide with QTL for smoltification and salinity tolerance traits in rainbow trout. The effects of body size QTL appear to be independent of changes in ambient salinity.

Whole genome duplication: challenges and considerations associated with sequence orthology assignment in Salmoninae

To illustrate some of the challenges and considerations in assigning correct orthology necessary for any comparative genomic investigation among salmonids, sequence data from the non-coding regions of different chromosomes in three members of the subfamily Salmoninae, rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar and Arctic charr Salvelinus alpinus, were compared. By analysing c. 55 distinct loci, corresponding to c. 142 kbp sequence information per species, 18 duplicated patterns representative of the two sequential rounds of teleost-specific whole genome duplications (i.e. 3R and 4R WGD) were identified. Sequence similarities between the 4R paralogues were c. 90%, which was slightly lower than those of the 4R orthologues and c. 60% for the 3R products. Through careful examination of the sequence data, however, only 14 loci could reliably be assigned as true orthologues. Locus-specific trees were constructed through maximum parsimony, maximum likelihood and neighbour-joining methods and were rooted using the information from a close relative, lake whitefish Coregonus clupeaformis. All approaches generated congruent trees supporting the {Coregonus [Salmo (Oncorhynchus, Salvelinus)]} topology. The general phenotypic characteristics of sequences, however, were highly suggestive of the basal position of Oncorhynchus, raising the hypothesis of an accelerated rate of nucleotide evolution in this species.

Genome evolution in the fish family salmonidae: generation of a brook charr genetic map and comparisons among charrs (Arctic charr and brook charr) with rainbow trout

BACKGROUND

Salmonids are regarded as 4R derivative species, having experienced 4 whole genome duplication events in their ancestry. Many duplicated chromosome regions still share extensive homology with one another which is maintained primarily through male-based homeologous chromosome pairings during meiosis. The formation of quadrivalents during meiosis leads to pseudolinkage. This phenomenon is more prevalent within 5 of the 12 ancestral teleost linkage groups in salmonids.

RESULTS

We constructed a genetic linkage map for brook charr and used this in combination with the genetic map from Arctic charr, to make comparisons with the genetic map of rainbow trout. Although not all chromosome arms are currently mapped, some homologous chromosome rearrangements were evident between Arctic charr and brook charr. Notably, 10 chromosome arms in brook charr representing 5 metacentric chromosomes in Arctic charr have undergone rearrangements. Three metacentrics have one arm translocated and fused with another chromosome arm in brook charr to a make a new metacentrics while two metacentrics are represented by 4 acrocentric pairs in brook charr. In two cases (i.e., BC-4 and BC-16), an apparent polymorphism was observed with the identification of both a putative metacentric structure (similar to metacentric AC-4 = BC-4 and a joining of acrocentric AC-16 + one arm of AC-28 = BC-16), as well as two separate acrocentric linkage groups evident in the mapping parents. Forty-six of the expected 50 karyotypic arms could be inter-generically assigned. SEX in brook charr (BC-4) was localized to the same homologous linkage group region as in Arctic charr (AC-4). The homeologous affinities detected in the two charr species facilitated the identification of 20 (expected number = 25) shared syntenic regions with rainbow trout, although it is likely that some of these regions were partial or overlapping arm regions.

CONCLUSIONS

Inter-generic comparisons among 2 species of charr (genus Salvelinus) and a trout (genus Oncorhynchus) have identified that linkage group arm arrangements are largely retained among these species. Previous studies have revealed that up to 7 regions of high duplicate marker retention occur between Salmo species (i.e., Atlantic salmon and brown trout) and rainbow trout, with 5 of these regions exhibiting higher levels of pseudolinkage. Pseudolinkage was detected in the charr species (i.e., BC-1/21, AC-12/27, AC-6/23, = RT-2p/29q, RT-12p/16p, and RT-27p/31p, respectively) consistent with three of the five 'salmonid-specific' pseudolinkage regions. Chromosome arms with the highest number of duplicated markers in rainbow trout are the linkage group arms with the highest retention of duplicated markers in both charr species.

Genetic architecture of body weight, condition factor and age of sexual maturation in Icelandic Arctic charr (Salvelinus alpinus)

The high commercial value from the aquaculture of salmonid fishes has prompted many studies into the genetic architecture of complex traits and the need to identify genomic regions that have repeatable associations with trait variation both within and among species. We searched for quantitative trait loci (QTL) for body weight (BW), condition factor (CF) and age of sexual maturation (MAT) in families of Arctic charr (Salvelinus alpinus) from an Icelandic breeding program. QTL with genome-wide significance were detected for each trait on multiple Arctic charr (AC) linkage groups (BW: AC-4, AC-20; CF: AC-7, AC-20, AC-23, AC-36; MAT: AC-13/34, AC-39). In addition to the genome-wide significant QTL for both BW and CF on AC-20, linkage groups AC-4, AC-7, AC-8, and AC-16 contain QTL for both BW and CF with chromosome-wide significance. These regions had effects (albeit weaker) on MAT with the exception of the region on AC-8. Comparisons with a North American cultured strain of Arctic charr, as well as North American populations of Atlantic salmon (Salmo salar), and rainbow trout (Oncorhynchus mykiss), reveal some conservation in QTL location and structure, particularly with respect to the joint associations of QTL influencing BW and CF. The detection of some differences in genetic architecture between the two aquaculture strains of Arctic charr may be reflective of the differential evolutionary histories experienced by these fishes, and illustrates the importance of including different strains to investigate genetic variation in a species where the intent is to use that variation in selective breeding programs.

Phenotypic plasticity, heterochrony and ontogenetic repatterning during juvenile development of divergent Arctic charr (Salvelinus alpinus)

Phenotypic plasticity is a developmental process that plays a role as a source of variation for evolution. Models of adaptive divergence make the prediction that increasing ecological specialization should be associated with lower levels of plasticity. We tested for differences in the magnitude, rate and trajectory of morphological plasticity in two lake populations of Arctic charr (Salvelinus alpinus) that exhibited variation in the degree of resource polymorphism. We reared offspring on diet treatments that mimicked benthic and pelagic prey. Offspring from the more divergent population had lower levels of morphological plasticity. Allometry influenced the rate of shape change over ontogeny, with differences in rate among ecomorphs being minimal when allometric variation was removed. However, plasticity in the spatial trajectory of development was extensive across ecomorphs, both with and without the inclusion of allometric variation, suggesting that different aspects of shape development can evolve independently.

Formulation and stability of pilocarpine oral solution

The stability of four formulations of pilocarpine oral solution containing glycerol, hydroxybenzoate preservatives and lemon spirit was studied on storage for 90 days at 4, 25 and 38C using a stability-indicating high performance liquid chromatography assay. The solutions were prepared from pilocarpine hydrochloride powder (0.2 and 3mg/ml) in citrate buffer pH 5.5, or from eyedrops (3mg/ml) in citrate buffer pH 5.5 or phosphate buffer pH 7.5. Significant decomposition of pilocarpine occurred in the pH 7.5 formulation at all three temperatures. The data were adequately described by a first order model. Degradation in the pH 5.5 formulations was not significant over 90 days at 4C or 60 days at 25C. Decomposition at 38C was significant and adequately described by a zero order model. The lower 95 per cent confidence limits for 10 per cent decomposition were 36 days for the eye-drop formulation and 27 and 32 days for the 0.2 and 3mg/ml powder formulations respectively. Pilocarpine oral solution prepared from powder or eye-drops in pH 5.5 buffer is chemically stable for 60 or 90 days at 25C or 4C, respectively, and provides a stable dosage form.

The genetic architecture of embryonic developmental rate and genetic covariation with age at maturation in rainbow trout Oncorhynchus mykiss

The genetic architecture underlying variation in embryonic developmental rate (DR) and genetic covariation with age of maturation (MAT) was investigated in rainbow trout Oncorhynchus mykiss. Highly significant additive parental effects and more limited evidence of epistatic effects on progeny hatching time were detected in three diallel sets of families. Genome scans with an average of 142 microsatellite loci from all 29 linkage groups in two families detected significant quantitative trait loci (QTL) for developmental rate on RT-8 and RT-30 with genome-wide and chromosome-wide effects, respectively. The QTL on linkage group RT-8 explained 23·7% of the phenotypic variation and supports results from previous studies. The co-localization of QTL for both DR and MAT to several linkage groups and the observation that alleles associated with faster developmental rate were found significantly more often in early maturing rather than typical and later maturing male ancestors supports the hypothesis of genetic covariation between DR and MAT. The maturation background and schedule of additional sires, however, did not have a consistent association with their progeny hatching times, suggesting that other genetic, environmental and physiological effects contribute to variation in these life-history traits.

Evolution of adaptive diversity and genetic connectivity in Arctic charr (Salvelinus alpinus) in Iceland

The ecological theory of adaptive radiation predicts that the evolution of phenotypic diversity within species is generated by divergent natural selection arising from different environments and competition between species. Genetic connectivity among populations is likely also to have an important role in both the origin and maintenance of adaptive genetic diversity. Our goal was to evaluate the potential roles of genetic connectivity and natural selection in the maintenance of adaptive phenotypic differences among morphs of Arctic charr, Salvelinus alpinus, in Iceland. At a large spatial scale, we tested the predictive power of geographic structure and phenotypic variation for patterns of neutral genetic variation among populations throughout Iceland. At a smaller scale, we evaluated the genetic differentiation between two morphs in Lake Thingvallavatn relative to historically explicit, coalescent-based null models of the evolutionary history of these lineages. At the large spatial scale, populations are highly differentiated, but weakly structured, both geographically and with respect to patterns of phenotypic variation. At the intralacustrine scale, we observe modest genetic differentiation between two morphs, but this level of differentiation is nonetheless consistent with strong reproductive isolation throughout the Holocene. Rather than a result of the homogenizing effect of gene flow in a system at migration-drift equilibrium, the modest level of genetic differentiation could equally be a result of slow neutral divergence by drift in large populations. We conclude that contemporary and recent patterns of restricted gene flow have been highly conducive to the evolution and maintenance of adaptive genetic variation in Icelandic Arctic charr.

Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling

Background

Clock family genes encode transcription factors that regulate clock-controlled genes and thus regulate many physiological mechanisms/processes in a circadian fashion. Clock1 duplicates and copies of Clock3 and NPAS2-like genes were partially characterized (genomic sequencing) and mapped using family-based indels/SNPs in rainbow trout (RT)(Oncorhynchus mykiss), Arctic charr (AC)(Salvelinus alpinus), and Atlantic salmon (AS)(Salmo salar) mapping panels.

Results

Clock1 duplicates mapped to linkage groups RT-8/-24, AC-16/-13 and AS-2/-18. Clock3/NPAS2-like genes mapped to RT-9/-20, AC-20/-43, and AS-5. Most of these linkage group regions containing the Clock gene duplicates were derived from the most recent 4R whole genome duplication event specific to the salmonids. These linkage groups contain quantitative trait loci (QTL) for life history and growth traits (i.e., reproduction and cell cycling). Comparative synteny analyses with other model teleost species reveal a high degree of conservation for genes in these chromosomal regions suggesting that functionally related or co-regulated genes are clustered in syntenic blocks. For example, anti-müllerian hormone (amh), regulating sexual maturation, and ornithine decarboxylase antizymes (oaz1 and oaz2), regulating cell cycling, are contained within these syntenic blocks.

Conclusions

Synteny analyses indicate that regions homologous to major life-history QTL regions in salmonids contain many candidate genes that are likely to influence reproduction and cell cycling. The order of these genes is highly conserved across the vertebrate species examined, and as such, these genes may make up a functional cluster of genes that are likely co-regulated. CLOCK, as a transcription factor, is found within this block and therefore has the potential to cis-regulate the processes influenced by these genes. Additionally, clock-controlled genes (CCGs) are located in other life-history QTL regions within salmonids suggesting that at least in part, trans-regulation of these QTL regions may also occur via Clock expression.

Growth-related quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss)

Background

Somatic growth is a complex process that involves the action and interaction of genes and environment. A number of quantitative trait loci (QTL) previously identified for body weight and condition factor in rainbow trout (Oncorhynchus mykiss), and two other salmonid species, were used to further investigate the genetic architecture of growth-influencing genes in this species. Relationships among previously mapped candidate genes for growth and their co-localization to identified QTL regions are reported. Furthermore, using a comparative genomic analysis of syntenic rainbow trout linkage group clusters to their homologous regions within model teleost species such as zebrafish, stickleback and medaka, inferences were made regarding additional possible candidate genes underlying identified QTL regions.

Results

Body weight (BW) QTL were detected on the majority of rainbow trout linkage groups across 10 parents from 3 strains. However, only 10 linkage groups (i.e., RT-3, -6, -8, -9, -10, -12, -13, -22, -24, -27) possessed QTL regions with chromosome-wide or genome-wide effects across multiple parents. Fewer QTL for condition factor (K) were identified and only six instances of co-localization across families were detected (i.e. RT-9, -15, -16, -23, -27, -31 and RT-2/9 homeologs). Of note, both BW and K QTL co-localize on RT-9 and RT-27. The incidence of epistatic interaction across genomic regions within different female backgrounds was also examined, and although evidence for interaction effects within certain QTL regions were evident, these interactions were few in number and statistically weak. Of interest, however, was the fact that these predominantly occurred within K QTL regions. Currently mapped growth candidate genes are largely congruent with the identified QTL regions. More QTL were detected in male, compared to female parents, with the greatest number evident in an F₁ male parent derived from an intercross between domesticated and wild strain of rainbow trout which differed strongly in growth rate.

Conclusions

Strain background influences the degree to which QTL effects are evident for growth-related genes. The process of domestication (which primarily selects faster growing fish) may largely reduce the genetic influences on growth-specific phenotypic variation. Although heritabilities have been reported to be relatively high for both BW and K growth traits, the genetic architecture of K phenotypic variation appears less defined (i.e., fewer major contributing QTL regions were identified compared with BW QTL regions).

Marker-assisted determination of the relationship between body size and reproductive success and consequences for evaluation of adaptive life histories

We tested for differences in the predicted optimal ages at first maturity in brook charr (Salvelinus fontinalis) in Freshwater River, Newfoundland, when life-history data were collated based on the marker-assisted estimation of the relationship between body size and reproductive success rather than using fecundity as a surrogate for reproductive success. Jointly with capture-recapture data to estimate the growth and survival costs of reproduction, we found that weak relationships between body size and reproductive success generate selection against delayed maturation. This finding would not have held for females if the relationship between body size and fecundity had been used as a surrogate for the relationship between body size and reproductive success. This shows that predictions of optimal life histories can be qualitatively changed when using molecular markers to directly evaluate age- and/or size-specific effects of body size on reproductive success.

Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout

Background

Recent advances in the accumulation of genetic mapping and DNA sequence information from several salmonid species support the long standing view of an autopolyploid origin of these fishes (i.e., 4R). However, the paralogy relationships of the chromosomal segments descendent from earlier polyploidization events (i.e., 2R/3R) largely remain unknown, mainly due to an unbalanced pseudogenization of paralogous genes that were once resident on the ancient duplicated segments. Inter-specific conserved noncoding elements (CNE) might hold the key in identifying these regions, if they are associated with arrays of genes that have been highly conserved in syntenic blocks through evolution. To test this hypothesis, we investigated the chromosomal positions of subset of CNE in the rainbow trout genome using a comparative genomic framework.

Results

Through a genome wide analysis, we selected 41 pairs of adjacent CNE located on various chromosomes in zebrafish and obtained their intervening, less conserved, sequence information from rainbow trout. We identified 56 distinct fragments corresponding to about 150 Kbp of sequence data that were localized to 67 different chromosomal regions in the rainbow trout genome. The genomic positions of many duplicated CNE provided additional support for some previously suggested homeologies in this species. Additionally, we now propose 40 new potential paralogous affinities by analyzing the variation in the segregation patterns of some multi-copy CNE along with the synteny association comparison using several model vertebrates. Some of these regions appear to carry signatures of the 1R, 2R or 3R duplications. A subset of these CNE markers also demonstrated high utility in identifying homologous chromosomal segments in the genomes of Atlantic salmon and Arctic charr.

Conclusion

CNE seem to be more efficacious than coding sequences in providing insights into the ancient paralogous affinities within the vertebrate genomes. Such a feature makes these elements extremely attractive for comparative genomics studies, as they can be treated as 'anchor' markers to investigate the association of distally located candidate genes on the homologous genomic segments of closely or distantly related organisms.

Determination of quantitative trait loci (QTL) for early maturation in rainbow trout (Oncorhynchus mykiss)

To identify quantitative trait loci (QTL) influencing early maturation (EM) in rainbow trout (Oncorhynchus mykiss), a genome scan was performed using 100 microsatellite loci across 29 linkage groups. Six inter-strain paternal half-sib families using three inter-strain F(1) brothers (approximately 50 progeny in each family) derived from two strains that differ in the propensity for EM were used in the study. Alleles derived from both parental sources were observed to contribute to the expression of EM in the progeny of the brothers. Four genome-wide significant QTL regions (i.e., RT-8, -17, -24, and -30) were observed. EM QTL detected on RT-8 and -24 demonstrated significant and suggestive QTL effects in both male and female progeny. Furthermore, within both male and female full-sib groupings, QTL on RT-8 and -24 were detected in two or more of the five parents used. Significant genome-wide and several strong chromosome-wide QTL for EM localized to different regions in males and females, suggesting some sex-specific control. Namely, QTL detected on RT-13, -15, -21, and -30 were associated with EM only in females, and those on RT-3, -17, and -19 were associated with EM only in males. Within the QTL regions identified, a comparison of syntenic EST markers from the rainbow trout linkage map with the zebrafish (Danio rerio) genome identified several putative candidate genes that may influence EM.

A framework for power and sensitivity analyses for quantitative genetic studies of natural populations, and case studies in Soay sheep (Ovis aries)

Studies of the quantitative genetics of natural populations have contributed greatly to evolutionary biology in recent years. However, while pedigree data required are often uncertain (i.e. incomplete and partly erroneous) and limited, means to evaluate the effects of such uncertainties have not been developed. We have therefore developed a general framework for power and sensitivity analyses of such studies. We propose that researchers first generate a set of pedigree data that they wish to use in a quantitative genetic study, as well as data regarding errors that occur in that pedigree. This pedigree is then permuted using the data regarding errors to generate hypothetical 'true' and 'assumed' pedigrees that differ so as to mimic pedigree errors that might occur in the study system under consideration. Phenotypic data are then simulated across the true pedigree (according to user-defined genetic and environmental covariance structures), before being analysed with standard quantitative genetic techniques in conjunction with the 'assumed' pedigree data. To illustrate this approach, we conducted power and sensitivity analyses in a well-known study of Soay sheep (Ovis aries). We found that, although the estimation of simple genetic (co)variance structures is fairly robust to pedigree errors, some potentially serious biases were detected under more complex scenarios involving maternal effects. Power analyses also showed that this study system provides high power to detect heritabilities as low as about 0.09. Given this range of results, we suggest that such power and sensitivity analyses could greatly complement empirical studies, and we provide the computer program PEDANTICS to aid in their application.

Genomic organization of the IGF1, IGF2, MYF5, MYF6 and GRF/PACAP genes across Salmoninae genera

Whole-genome duplication in the ancient ray-finned fish and subsequent tetraploidization in the ancestor to the salmonids have complicated genomic and candidate gene studies in these organisms as many genes with multiple copies are present throughout their genomes. In an attempt to identify genes with a potential influence on growth and development, we investigated the genomic positions of insulin-like growth factors 1 and 2 (IGF1, IGF2), myogenic factors 5 and 6 (MYF5, MYF6) and growth hormone-releasing factor/pituitary adenylate cyclase-activating polypeptide (GRF/PACAP) in three salmonid species: rainbow trout (Oncorhynchus mykiss), Atlantic salmon (Salmo salar) and Arctic charr (Salvelinus alpinus). Our results suggest a tight association between the IGF1, MYF5 and MYF6 genes in all three species. We further localized the duplicated copies of IGF1 to the homeologous linkage groups RT-7/15 in rainbow trout and AC-3/24 in Arctic charr, and the two copies of MYF6 to homeologous linkage groups AS-22/24 in Atlantic salmon. Localization of GRF/PACAP to RT-7, AS-31 and AC-27 and IGF2 to RT-27, AS-2 and AC-4 in rainbow trout, Atlantic salmon and Arctic charr respectively is consistent with previously reported homologies among these chromosomal segments identified using other genetic markers. However, localization of the second copy of GRF/PACAP to RT-19 and AC-14 and the duplicated copy of IGF2 to AC-19 suggest a possible new homology/homeology between these chromosomes. These results might also be an indication of a more ancient polyploidization event that occurred deep in the ray-finned fish lineage.

Genome organization of glutamine synthetase genes in rainbow trout (Oncorhynchus mykiss)

Unlike mammals, bony fish appear to possess multiple genes encoding glutamine synthetase (GS), the nitrogen metabolism enzyme responsible for the conversion of glutamate and ammonia into glutamine at the expense of ATP. This study reports on the development of genetic markers for each of the four isoforms identified thus far in rainbow trout (Oncorhynchus mykiss) and their genome localization by linkage mapping. We found that genes coding for GS01, GS02, GS03, and GS04 map to four different linkage groups in the trout genome, namely RT-24, RT-23, RT-08, and RT-13, respectively. Linkage groups RT-23 and RT-13 appear to represent distinct chromosomes sharing duplicated marker regions, which lends further support to the previous suggestion that GS02 and GS04 may be duplicate gene copies that evolved from a whole-genome duplication in the trout ancestor. In contrast, there is at present no further evidence that RT-24 and RT-08 share ancestrally homologous segments and additional genomic studies will be needed to clarify the evolutionary origin of genes coding for GS01 and GS03.

Quantitative trait loci for body weight, condition factor and age at sexual maturation in Arctic charr (Salvelinus alpinus): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar)

In salmonid fishes, life-history changes may often be coupled to early individual growth trajectories. We identified quantitative trait loci (QTL) for body weight (BW), condition factor (K) and age at sexual maturation (MT) in two full-sib families of Arctic charr (Salvelinus alpinus) to ascertain if QTL for MT were confounded with BW QTL intervals. Three significant QTL for BW, three QTL for MT and one significant QTL for K were identified. A BW QTL with major effect was localized to linkage group 8 (AC-8) and explained more than 34% of the phenotypic variation. Markers on AC-8 have previously been identified as being associated with variation in fork length and BW in this species. Similarly, a major QTL (PEV = 23%) with an influence on the female MT was localized to AC-23. Some of these regions are homologous to those in the genomes of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar), where similar QTL effects have been detected. Our results also suggest the conservation of MT QTL on the homeologous linkage group pair AC-3/24 in Arctic charr. We further identified chromosomal regions that harbor QTL for multiple traits. In particular, markers on AC-4, -20 and -36 had detectable QTL for all traits studied. Significant MT QTL detected on AC-23, -24, and -27 were autonomous of any BW QTL regions, suggesting that the regulation of MT may be more independent of BW control within this species than in other species of salmonids.

Multiple hyperechoic testicular lesions are a common finding on ultrasound in Cowden disease and represent lipomatosis of the testis

Cowden disease (CD) is a genetic disease associated with multiple hamartomas and malignant neoplasms. During investigations for possible subnormal fertility, a series of eight males with CD underwent ultrasound scanning of their testes. Our findings detail the seven adult patients that were found to have multiple and bilateral testicular lesions on ultrasound. These lesions in Cowden's patients represent a newly described testicular pathology - lipomatosis of the testis. Here we detail the radiological findings. Ultrasound findings showed multiple (estimated 40+) discreet lesions randomly scattered thoughout the parenchyma of each affected testis. The lesions themselves had heterogeneous echo texture, but all being hyperechoic and with a variable size from 1 mm to 6 mm. One patient underwent MR examination of the lesions in which a high T(1) signal was seen, but no useful characteristic features were identifiable.

A linkage map for brown trout (Salmo trutta): chromosome homeologies and comparative genome organization with other salmonid fish

We report on the construction of a linkage map for brown trout (Salmo trutta) and its comparison with those of other tetraploid-derivative fish in the family Salmonidae, including Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), and Arctic char (Salvelinus alpinus). Overall, we identified 37 linkage groups (2n = 80) from the analysis of 288 microsatellite polymorphisms, 13 allozyme markers, and phenotypic sex in four backcross families. Additionally, we used gene-centromere analysis to approximate the position of the centromere for 20 linkage groups and thus relate linkage arrangements to the physical morphology of chromosomes. Sex-specific maps derived from multiple parents were estimated to cover 346.4 and 912.5 cM of the male and female genomes, respectively. As previously observed in other salmonids, recombination rates showed large sex differences (average female-to-male ratio was 6.4), with male crossovers generally localized toward the distal end of linkage groups. Putative homeologous regions inherited from the salmonid tetraploid ancestor were identified for 10 pairs of linkage groups, including five chromosomes showing evidence of residual tetrasomy (pseudolinkage). Map alignments with orthologous regions in Atlantic salmon, rainbow trout, and Arctic char also revealed extensive conservation of syntenic blocks across species, which was generally consistent with chromosome divergence through Robertsonian translocations.

The candidate gene, Clock, localizes to a strong spawning time quantitative trait locus region in rainbow trout

We applied a candidate gene mapping approach to an existing quantitative trait loci (QTL) data set for spawning date in rainbow trout (Oncorynchus mykiss) to ascertain whether these genes could potentially account for any observed QTL effects. Several genes were chosen for their known or suspected roles in reproduction, circadian, or circannual timing, including salmon-type gonadotropin-releasing hormone 3A and 3B (GnRH3A and GnRH3B), Clock, Period1, and arylalkylamine N-acetlytransferase-1 and -2 (AANAT-1 and AANAT-2). Genes were sequenced, and polymorphisms were identified in parents of two rainbow trout mapping families, one of which was used previously to detect spawn timing QTL. Interval mapping was used to identify associations between genetic markers and spawning date effects. Using a genetic map that was updated with 574 genetic markers (775 total), we found evidence for 11 significant or suggestive QTL regions. Most QTL were only localized within one of the parents; however, a strong QTL region was identified in both female and male parents on linkage group RT-8 that explained 20% and 50% of trait variance, respectively. The Clock gene mapped to this region. Period1 mapped to a region in the female parent associated with a marginal effect (P = .056) on spawn timing. Other candidate genes were not associated with significant QTL effects.

A physical map of the genome of Atlantic salmon, Salmo salar

A physical map of the Atlantic salmon (Salmo salar) genome was generated based on HindIII fingerprints of a publicly available BAC (bacterial artificial chromosome) library constructed from DNA isolated from a Norwegian male. Approximately 11.5 haploid genome equivalents (185,938 clones) were successfully fingerprinted. Contigs were first assembled via FPC using high-stringency (1e-16), and then end-to-end joins yielded 4354 contigs and 37,285 singletons. The accuracy of the contig assembly was verified by hybridization and PCR analysis using genetic markers. A subset of the BACs in the library contained few or no HindIII recognition sites in their insert DNA. BglI digestion fragment patterns of these BACs allowed us to identify three classes: (1) BACs containing histone genes, (2) BACs containing rDNA-repeating units, and (3) those that do not have BglI recognition sites. End-sequence analysis of selected BACs representing these three classes confirmed the identification of the first two classes and suggested that the third class contained highly repetitive DNA corresponding to tRNAs and related sequences.

A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae)

We updated the genetic map of rainbow trout (Oncorhynchus mykiss) for 2 outcrossed mapping panels, and used this map to assess the putative chromosome structure and recombination rate differences among linkage groups. We then used the rainbow trout sex-specific maps to make comparisons with 2 other ancestrally polyploid species of salmonid fishes, Arctic charr (Salvelinus alpinus) and Atlantic salmon (Salmo salar) to identify homeologous chromosome affinities within each species and ascertain homologous chromosome relationships among the species. Salmonid fishes exhibit a wide range of sex-specific differences in recombination rate, with some species having the largest differences for any vertebrate species studied to date. Our current estimate of female:male recombination rates in rainbow trout is 4.31:1. Chromosome structure and (or) size is associated with recombination rate differences between the sexes in rainbow trout. Linkage groups derived from presumptive acrocentric type chromosomes were observed to have much lower sex-specific differences in recombination rate than metacentric type linkage groups. Arctic charr is karyotypically the least derived species (i.e., possessing a high number of acrocentric chromosomes) and Atlantic salmon is the most derived (i.e., possessing a number of whole-arm fusions). Atlantic salmon have the largest female:male recombination ratio difference (i.e., 16.81:1) compared with rainbow trout, and Arctic charr (1.69:1). Comparisons of recombination rates between homologous segments of linkage groups among species indicated that when significant experiment-wise differences were detected (7/24 tests), recombination rates were generally higher in the species with a less-derived chromosome structure (6/7 significant comparisons). Greater similarity in linkage group syntenies were observed between Atlantic salmon and rainbow trout, suggesting their closer phylogenetic affinities, and most interspecific linkage group comparisons support a model that suggests whole chromosome arm translocations have occurred in the evolution of this group. However, some possible exceptions were detected and these findings are discussed in relation to their influence on segregation distortion patterns. We also report unusual meiotic segregation patterns in a female parent involving the duplicated (homeologous) linkage group pair 12/16 and discuss several models that may account for these patterns.Key words: linkage analysis, genetic markers, polyploidy, tetrasomic inheritance, segregation distortion, recombination rate.