Characterization of sex chromosomes in rainbow trout and coho salmon using fluorescence in situ hybridization (FISH)

With the aim of characterizing the sex chromosomes of rainbow trout (Oncorhynchus mykiss) and to identify the sex chromosomes of coho salmon (O. kisutch), we used molecular markers OmyP9, 5S rDNA, and a growth hormone gene fragment (GH2), as FISH probes. Metaphase chromosomes were obtained from lymphocyte cultures from farm specimens of rainbow trout and coho salmon. Rainbow trout sex marker OmyP9 hybridizes on the sex chromosomes of rainbow trout, while in coho salmon, fluorescent signals were localized in the medial region of the long arm of one subtelocentric chromosome pair. This hybridization pattern together with the hybridization of a GH2 intron probe on a chromosome pair having the same morphology, suggests that a subtelocentric pair could be the sex chromosomes in this species. We confirm that in rainbow trout, one of the two loci for 5S rDNA genes is on the X chromosome. In males of this species that lack a heteromorphic sex pair (XX males), the 5S rDNA probe hybridized to both subtelocentrics This finding is discussed in relation to the hypothesis of intraspecific polymorphism of sex chromosomes in rainbow trout.     

Chromosome size in salmon and trout

The chromosomes of the Atlantic salmon, Salmo salar (2n=58) are, on average, larger than those of the trout, S. trutta (2n=80). If the difference in chromosome size represents a permanent change in chromosome structure as between the two species the expectation is that the size difference between salmon and trout chromosomes will be maintained in the hybrid. If, alternatively, the size difference between salmon and trout chromosomes is genotypically determined the difference will not be maintained in nuclei of hybrid genotype. Measurements of a specific chromosome, S, of the salmon complement and of another, S ¹, of the trout complement in nuclei of parent species and of the hybrid show that the difference in size is maintained in hybrid nuclei. It is concluded therefore that the size difference between salmon and trout chromosomes is due to structural change rather than to genotypic control.     

Isolation and cross‐familial amplification of 41 microsatellites for the brook charr (Salvelinus fontinalis)

The brook charr (Salvelinus fontinalis; Osteichthyes: Salmonidae) is a phenotypically diverse fish species inhabiting much of North America. But relatively few genetic diagnostic resources are available for this fish species. We isolated 41 microsatellites from S. fontinalis polymorphic in one or more species of salmonid fish. Thirty‐seven were polymorphic in brook charr, 15 in the congener Arctic charr (Salvelinus alpinus) and 14 in the lake charr (Salvelinus namaycush). Polymorphism was also relatively high in Oncorhynchus, where 21 loci were polymorphic in rainbow trout (Oncorhynchus mykiss) and 16 in cutthroat trout (Oncorhynchus clarkii) but only seven and four microsatellite loci were polymorphic in the more distantly related lake whitefish (Coregonus clupeaformis) and Atlantic salmon (Salmo salar), respectively. One duplicated locus (Sfo228Lav) was polymorphic at both duplicates in S. fontinalis.     

Characterization of Charr Chromosomes Using Fluorescence in Situ Hybridization

The chromosomal locations of several families of tandem repetitive DNA sequences and the 5S rDNA were determined using fluorescence in situ hybridization (FISH) in the five North American charr species: Salvelinus namaycush, S. fontinalis, S. alpinus, S. malma, and S. confluentus. The pattern of hybridization of three centromeric repetitive sequences previously isolated from S. namaycush and S. alpinus was unique in each species. Dual-color FISH experiments showed that in several species many of the centromeres had the EcoRI-DraI family in addition to either the AluI-RsaI type A or type B families. The EcoRI-DraI family which was found only at the centromeres of acrocentric chromosomes in S. namaycush, S. fontinalis and S. malma was also found at centromeres of selected metacentrics in S. alpinus (one pair) and S. confluentus (four pairs) whose chromosomes have undergone additional centric fusions compared to the other species. The locations of 5S rDNA sequences were different in each species except for the two most closely related (S. alpinus and S. malma). Two whole-arm chromosome paint probes, one specific for the short and the other for the long arm of the lake charr sex chromosomes, hybridize to the same chromosome pair in all species. Results with other paint probes suggest that independent centric fusions have occurred in S. alpinus and S. confluentus which is consistent with the phylogenetic tree obtained previously for Salvelinus with cytogenetic and DNA data.     

Special traits of biology and of the parasite fauna of juvenile salmonid fish of the genus <Emphasis Type="Italic">Salmo</Emphasis> of the Tornio River system (The Baltic Sea basin)

Juveniles of Atlantic salmon Salmo salar and trout S. trutta populating the system of the Tornio River (the Baltic Sea basin) are investigated. The obtained parasitological data indicate the absence of rigid spatial and food competition between juvenile salmon and trout in the case of their cohabitation.     

A triose-phosphate isomerase polymorphism in the Atlantic salmonSalmo salar L.

Atlantic salmon,Salmo salar L., from four European locations show allelic variation at one of three triose-phosphate isomerase (TPI) loci (TPI-3*) when separated on horizontal starch gel electrophoresis, using either eye or liver extracts. Two common alleles (*100 and*103) and one rare allele (*97) segregate atTPI-3* with unambiguous typing being possible by observing the interlocus heterodimers. Family studies demonstrate thatTPI-3* 100 and*103 are of autosomal location and are inherited in a Mendelian fashion.TPI-3* variation can also be typed in adipose fin tissue, allowing nondestructive tissue sampling. Three loci are also active in brown trout,Salmo trutta, with two individuals being homozygous forTPI-3*, as are a small number ofS. salar from eastern Canada. The presence of this additional variable allozyme locus inS. salar is important, since genetic studies in that species have been limited by the low level of allozyme variability detectable.     

Constitutive heterochromatin, 5S and 18S rDNA genes in Apareiodon sp. (Characiformes, Parodontidae) with a ZZ/ZW sex chromosome system

Karyotype, sex chromosome system and cytogenetics characteristics of an unidentified species of the genus Apareiodon originating from Piquiri River (Paraná State, Brazil) were investigated using differential staining techniques (C-banding and Ag-staining) and fluorescent in situ hybridization (FISH) with 5S and 18S rDNA probes. The diploid chromosome number was 2n = 54 with 25 pairs of meta- (m) to submetacentric (sm) and 2 pairs of subtelocentric (st) chromosomes. The major ribosomal rDNA sites as revealed by Ag-staining and FISH with 18S rDNA probe were found in distal region of longer arm of st chromosome pair 26, while minor 5S sites were observed in the interstitial sites on chromosome pairs 2 (smaller cluster) and 7 (larger one). The C-positive heterochromatin had pericentromeric and telomeric distribution. The heteromorphic sex chromosome system consisted of male ZZ (pair 21) and female middle-sized m/st Z/W chromosomes. The pericentric inversion of heterochromatinized short arm of ancestral Z followed by multiplication of heterochromatin segments is hypothesized for origin of W chromosome. The observed karyotype and chromosomal markers corresponded to those found in other species of the genus.     

Chromosomal mapping of the major and minor ribosomal genes, (GATA)n and (TTAGGG)n by one-color and double-color FISH in the toadfish Halobatrachus didactylus (Teleostei: Batrachoididae)

The karyotype of Halobatrachus didactylus presents 46 chromosomes, composed of eight metacentric, 18 submetacentric, four subtelocentric, and 16 acrocentric chromosomes. The results of FISH showed that the major ribosomal genes were located in the terminal position of the short arm of a large submetacentric chromosome. They also showed a high variation in the hybridization signals. The products of amplification of 5S rDNA produced bands of about 420 pb. The PCR labeled products showed hybridization signals in the subcentromeric position of the long arm of a submetacentric chromosome of medium size. Double-color FISH indicated that the two ribosomal families are not co-located since they hybridizated in different chromosomal pairs. Telomeres of all the chromosomes hybridized with the (TTAGGG) _n probe. The GATA probe displayed a strong signal in the long arm of a submetacentric chromosome of medium size, in the subcentromeric position. The double-color FISH showed that the microsatellite GATA and the 5S rDNA gene are located in different chromosomal pairs. The majority presence of GATA probes in one pair of chromosomes is unusual and considering its distribution through different taxa it could be due to evolutionary mechanisms of heterochromatine accumulation, leading to the formation of differentiated sex chromosomes.     

Reproduction of interspecific hybrids of Atlantic salmon and brown trout in a stream environment

1. Reproduction between Atlantic salmon males and interspecific hybrid Salmo salar × Salmo trutta females was monitored in a controlled flow channel diverted from a south European river located at the edge of Atlantic salmon natural geographic distribution in Europe. 2. Post‐F1 hybrids were viable and survived in the wild, at least until dispersal from redds. After transfer to hatchery conditions, 67% survived into the second year. 3. The hybrids possessed 98 chromosomes: two sets of Atlantic salmon(2n = 58) and one set of brown trout (n = 40) chromosomes. 4. The existence of a low proportion of allotriploid individuals can be expected in rivers where Atlantic salmon and brown trout populations coexist.     

Predictability of multispecies competitive interactions in three populations of Atlantic salmon Salmo salar

Juvenile Atlantic salmon Salmo salar from three allopatric populations (LaHave, Sebago and Saint‐Jean) were placed into artificial streams with combinations of four non‐native salmonids: brown trout Salmo trutta, rainbow trout Oncorhynchus mykiss, Chinook salmon Oncorhynchus tshawytscha and coho salmon Oncorhynchus kisutch. Non‐additive effects, as evidenced by lower performance than predicted from weighted summed two‐species competition trials, were detected for S. salar fork length (L_F) and mass, but not for survival, condition factor or riffle use. These data support emerging theory on niche overlap and species richness as factors that can lead to non‐additive competition effects.     

Identification of the sex chromosome pair in chum salmon (Oncorhynchus keta) and pink salmon (Oncorhynchus gorbuscha)

Fluorescence in situ hybridization (FISH) using a probe to the male-specific GH-Y (growth hormone pseudogene) was used to identify the Y chromosome in the karyotypes of chum salmon (Oncorhynchus keta) and pink salmon (Oncorhynchus gorbuscha). The sex chromosome pair is a small acrocentric chromosome pair in chum salmon and the smallest metacentric chromosome pair in pink salmon. Both of these chromosome pairs are morphologically different from the sex chromosome pairs in chinook salmon (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch). The 5S rRNA genes are on multiple chromosome pairs including the sex chromosome pair in chum salmon, but at the centromeres of two autosomal metacentric pairs in pink salmon. The sex chromosome pairs and the chromosomal locations of the 5S rDNA appear to be different in all five of the North American Pacific salmon species and rainbow trout. The implications of these results for evolution of sex chromosomes in salmonids are discussed.     

Evolution of Hox Clusters in Salmonidae: A Comparative Analysis Between Atlantic Salmon (Salmo salar) and Rainbow Trout (Oncorhynchus mykiss)

We studied the genomic organization of Hox genes in Atlantic salmon (Salmo salar) and made comparisons to that in rainbow trout (Oncorhynchus mykiss), another member of the family Salmonidae. We used these two species to test the hypothesis that the Hox genes would provide evidence for a fourth round of duplication (4R) of this gene family given the recent polyploid ancestry of the salmonid fish. Thirteen putative Hox clusters were identified and 10 of these complexes were localized to the current Atlantic salmon genetic map. Syntenic regions with the rainbow trout linkage map were detected and further homologies and homeologies are suggested. We propose that the common ancestor of Atlantic salmon and rainbow trout possessed at least 14 clusters of Hox genes, and additional clusters cannot be ruled out. Salmonid Hox cluster complements seem to be more similar to those of zebrafish (Danio rerio) than medaka (Oryzias latipes) or pufferfish (Sphoeroides nephelus and Takifugu rubripes), as both Atlantic salmon and rainbow trout have retained HoxCb ortholog, which has been lost in medaka and pufferfish but not in zebrafish. However, our data suggest that phylogenetically, the homologous genes within each cluster express mosaic relationships among the teleosts tested and, thus, leave unresolved the interfamilial relationships among these taxa. Sequence data from this article have been deposited within the EMBL/GenBank Data Libraries under the following accession numbers: AY677341, AY677342, AY677343, AY677344, AY677345, AY677346, AY677347, AY677348, AY677349, AY677350, AY677351, AY677352, AY677353, AY677354, AY677355, AY677356, AY677357, AY677358, AY677359, AY677360, AY677361, AY677362, AY677363, AY677364 and AY677365. [Reviewing Editor: Dr. Axel Meyer]     

Effects of salmon lice infection and salmon lice protection on fjord migrating Atlantic salmon and brown trout post-smolts

Effects of artificial salmon lice infection and pharmaceutical salmon lice prophylaxis on survival and rate of progression of Atlantic salmon (n = 72) and brown trout post-smolts (n = 72) during their fjord migration, were studied by telemetry. The infected groups were artificially exposed to infective salmon lice larvae in the laboratory immediately before release in the inner part of the fjord to simulate a naturally high infection pressure. Groups of infected Atlantic salmon (n = 20) and brown trout (n = 12) were also retained in the hatchery to control the infection intensity and lice development during the study period. Neither salmon lice infection nor pharmaceutical prophylaxis had any effects on survival and rate of progression of fjord migrating Atlantic salmon post-smolts compared to control fish. Atlantic salmon spent on average only 151.2 h (maximum 207.3 h) in passing the 80 km fjord system and had, thus, entered the ocean when the more pathogenic pre-adult and adult lice stages developed. The brown trout, in comparison to Atlantic salmon, remained to a larger extent than Atlantic salmon in the inner part of the fjord system. No effect of salmon lice infection, or protection, was found in brown trout during the first weeks of their fjord migration. Brown trout will, to a larger extent than Atlantic salmon, stay in the fjord areas when salmon lice infections reach the more pathogenic pre-adult and adult stages. In contrast to Atlantic salmon, they will thereby possess the practical capability of returning to freshwater when encountering severe salmon lice attacks.     

Phylogeny of Salmonine Fishes Based on Growth Hormone Introns: Atlantic (Salmo) and Pacific (Oncorhynchus) Salmon Are Not Sister Taxa

Though salmonid fishes are a well-studied group, phylogenetic questions remain, especially with respect to genus-level relationships. These questions were addressed with duplicate growth hormone (GH) introns. Intron sequences from each duplicate gene yielded phylogenetic trees that were not significantly different from each other in topology. Statistical tests supported validity of the controversial monotypic genusParahucho,monophyly ofOncorhynchus,and inclusion ofAcantholingua ohridanawithinSalmo.Suprisingly, GH1 intron C (GH1C) did not support the widely accepted hypothesis thatOncorhynchus(Pacific salmon and trout) andSalmo(Atlantic salmon and trout) are sibling genera; GH2C was ambiguous at this node. Previously published data were also examined for support ofSalmoandOncorhynchusas sister taxa and only morphology showed significant support. If not sister taxa, the independent evolution of anadromy—the migration to sea and return to freshwater for spawning—is most parsimonious. While there was incongruence with and among published data sets, the GH1C intron phylogeny was the best hypothesis, based on currently available molecular data.     

Identification of the sex chromosomes of brown trout (Salmo trutta) and their comparison with the corresponding chromosomes in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss)

Males are the heterogametic sex in salmonid fishes. In brown trout (Salmo trutta) the sex-determining locus, SEX, has been mapped to the end of linkage group BT-28, which corresponds to linkage group AS-8 and chromosome SSA15 in Atlantic salmon (Salmo salar). We set out to identify the sex chromosomes in brown trout. We isolated Atlantic salmon BAC clones containing microsatellite markers that are on BT-28 and also on AS-8, and used these BACs as probes for fluorescent in situ hybridization (FISH) analysis. SEX is located on the short arm of a small subtelocentric/acrocentric chromosome in brown trout, which is consistent with linkage analysis. The acrocentric chromosome SSA15 in Atlantic salmon appears to have arisen by a centric fusion of 2 small acrocentric chromosomes in the common ancestor of Salmo sp. We speculate that the fusion process that produced Atlantic salmon chromosome SSA15 disrupted the ancestral sex-determining locus in the Atlantic salmon lineage, providing the impetus either for the relocation of SEX or selection pressure for a novel sex-determining gene to arise in this species. Thus, the sex-determining genes may differ in Atlantic salmon and brown trout.     

Studies in individual spawnings of Salmo salar: a model to explain chromosome polymorphism patterns

Summary Atlantic salmon fry from nine offspring belonging to individual spawnings were karyotyped. Different patterns of Robertsonian chromosome polymorphism were obtained. A theoretical model is developed to explain the different chromosome polymorphism patterns in Salmo salar offspring in terms of the chromosome numbers of the parents.     

Chromosome relationships in the genus Salmo

Chromosome numbers and polymorphisms in rainbow trout, Atlantic salmon, and brown trout are described. The karyotypes of these three species are compared with each other and with those of other salmonid fish from the genera Salmo, Salvelinus, and Oncorhynchus. Karyotype evolution from a postulated ancestral tetraploid is discussed.     

Differences in pathogen resistance within and among cultured,conservation-dependent,and endangered populations of Atlantic salmon, <Emphasis Type="Italic">Salmo salar</Emphasis> L.

We report genetic differences for resistance to the pathogen Listonella anguillarum within and among one cultured and two wild Canadian populations of Atlantic salmon, Salmo salar, using a common-garden experimental protocol. Following exposure to the causative agent for vibriosis, parr originating from the endangered Stewiacke River population experienced significantly higher mortality than cultured parr, four generations removed from the Saint John River population, and wild parr from Tusket River. Pathogen resistance differed between sexes; males consistently experienced higher survival than females. There was no evidence that maturity influenced pathogen resistance in male parr. The population and sex differences in pathogen resistance documented here have implications for risk assessments of the demographic consequences of interbreeding between wild and farmed Atlantic salmon.     

Comparative diets and foraging strategies of subyearling Atlantic salmon,brown trout,and rainbow trout during winter

Over‐winter survival of salmonids in streams is thought to be an important population regulation mechanism. Yet because of the difficulty of conducting field studies due to adverse weather or ice conditions, compared to other seasons, salmonid ecology during winter is least understood. Consequently, we sought to examine interspecific feeding associations of an important salmonid stream assemblage in the Lake Ontario watershed during winter. The diets of Atlantic salmon (Salmo salar) parr, brown trout (S. trutta) parr, and rainbow trout (Oncorhynchus mykiss) parr were significantly different in February but not in March. Salmonid diets differed from the benthos and the drift during both months. Dipterans (chironomids, simuliids, and tipulids) and ephemerellids were the major prey taxa consumed. All three species fed more heavily on prey items from the benthos than from the drift. The diet of Atlantic salmon had the highest similarity to the benthos whereas the diet of brown trout had the lowest similarity to the drift. All three salmonid species generally selected ephemerellids, limnephilids, and chironomids and avoided elmids. These winter feeding observations are the first reported for this specific salmonid assemblage and will help managers better understand interspecific associations during this critical period.     

Genetic mapping of Y-chromosomal DNA markers in Pacific salmon

Sex chromosomes in fish provide an intriguing view of how sex-determination mechanisms evolve in vertebrates. Many fish species with single-factor sex-determination systems do not have cytogenetically-distinguishable sex chromosomes, suggesting that few sex-specific sequences or chromosomal rearrangements are present and that sex-chromosome evolution is thus at an early stage. We describe experiments examining the linkage arrangement of a Y-chromosomal GH pseudogene (GH-Y) sequence in four species of salmon (chum, Oncorhynchus keta; pink, O. gorbuscha; coho, O. kisutch; chinook, O. tshawytscha). Phylogenetic analysis indicates that GH-Y arose early in Oncorhynchus evolution, after this genus had diverged from Salmo and Salvelinus. However, GH-Y has not been detected in some Oncorhynchus species (O. nerka, O. mykiss and O. clarki), consistent with this locus being deleted in some lineages. GH-Y is tightly linked genetically to the sex-determination locus on the Y chromosome and, in chinook salmon, to another Y-linked DNA marker OtY1. GH-Y is derived from an ancestral GH2 gene, but this latter functional GH locus is autosomal or pseudoautosomal. YY chinook salmon are viable and fertile, indicating the Y chromosome is not deficient of vital genetic functions present on the X chromosome, consistent with sex chromosomes that are in an early stage of divergence.