Chromosomal differences between European and North American Atlantic salmon discovered by linkage mapping and supported by fluorescence in situ hybridization analysis

Background

Geographical isolation has generated a distinct difference between Atlantic salmon of European and North American Atlantic origin. The European Atlantic salmon generally has 29 pairs of chromosomes and 74 chromosome arms whereas it has been reported that the North American Atlantic salmon has 27 chromosome pairs and an NF of 72. In order to predict the major chromosomal rearrangements causing these differences, we constructed a dense linkage map for Atlantic salmon of North American origin and compared it with the well-developed map for European Atlantic salmon.

Results

The presented male and female genetic maps for the North American subspecies of Atlantic salmon, contains 3,662 SNPs located on 27 linkage groups. The total lengths of the female and male linkage maps were 2,153 cM and 968 cM respectively, with males characteristically showing recombination only at the telomeres. We compared these maps with recently published SNP maps from European Atlantic salmon, and predicted three chromosomal reorganization events that we then tested using fluorescence in situ hybridization (FISH) analysis. The proposed rearrangements, which define the differences in the karyotypes of the North American Atlantic salmon relative to the European Atlantic salmon, include the translocation of the p arm of ssa01 to ssa23 and polymorphic fusions: ssa26 with ssa28, and ssa08 with ssa29.

Conclusions

This study identified major chromosomal differences between European and North American Atlantic salmon. However, while gross structural differences were significant, the order of genetic markers at the fine-resolution scale was remarkably conserved. This is a good indication that information from the International Cooperation to Sequence the Atlantic salmon Genome, which is sequencing a European Atlantic salmon, can be transferred to Atlantic salmon from North America.

Comparative genome analysis of the primary sex-determining locus in salmonid fishes

We compared the Y-chromosome linkage maps for four salmonid species (Arctic charr, Salvelinus alpinus; Atlantic salmon, Salmo salar; brown trout, Salmo trutta; and rainbow trout, Oncorhynchus mykiss) and a putative Y-linked marker from lake trout (Salvelinus namaycush). These species represent the three major genera within the subfamily Salmoninae of the Salmonidae. The data clearly demonstrate that different Y-chromosomes have evolved in each of the species. Arrangements of markers proximal to the sex-determining locus are preserved on homologous, but different, autosomal linkage groups across the four species studied in detail. This indicates that a small region of DNA has been involved in the rearrangement of the sex-determining region. Placement of the sex-determining region appears telomeric in brown trout, Atlantic salmon, and Arctic charr, whereas an intercalary location for SEX may exist in rainbow trout. Three hypotheses are proposed to account for the relocation: translocation of a small chromosome arm; transposition of the sex-determining gene; or differential activation of a primary sex-determining gene region among the species.

Spawning success in Atlantic salmon (Salmo salarL.): a long-term DNA profiling-based study conducted in a natural stream

Spawning success of Atlantic salmon (Salmo salar L.) was investigated, under near-natural conditions, in the Girnock Burn, an 8-km long tributary of the River Dee in Scotland. Employing minisatellite-based DNA profiling, mating outcomes were resolved over three spawning seasons by assigning parentage to progeny samples removed from spawning nests ('redds'). While individual spawning patterns differed markedly, consistent trends were present over the 3 years studied. Multiple spawning was found to be prevalent. More than 50% of anadromous spawners of both sexes contributed to more than one redd. Up to six redds for a single female and seven for a single male were detected. Both sexes ranged extensively. Distance between redds involving the same parent varied from a few metres to > 5 km. Distances > 1 km were common. Both males and females ranged to a similar extent. Range limit was not correlated to fish size. Pairs were not monogamous, both males and females mating with different partners at different sites. Size assortative mating was apparent among 1991 spawners but was not detected for 1992 or 1995. Redd superimposition was found to be common (17-22% of redds over the 3 years), although it was not correlated to the number of anadromous spawners present. High levels of nonanadromous mature parr mating success (40-50% of total progeny sampled) were recorded, and these likely contribute greatly to the effective population size. The relevance of these findings at the individual and population level is discussed, with particular reference to management implications.

Physical localization and characterization of the BglI element in the genomes of Atlantic salmon (Salmo salar L.) and brown trout (S. trutta L.)

This work describes chromosomal localization, fine physical mapping, and population variation of the BglI element in the genome of Atlantic salmon (Salmo salar L.) and a similar sequence in the genome of brown trout (S. trutta L.). Results from a variety of complementary approaches, clearly demonstrate that the BglI element does not occur as a satellite-like repetitive DNA in these species but is part of the rDNA cistron as suggested by Goodier and Davidson (1993). Coincident hybridization of BglI clones with rDNA loci in both single and double-probe fluorescence in situ hybridization (FISH) experiments demonstrated physical linkage between the BglI element and rDNA loci. Fine physical mapping by Southern analysis and PCR amplification showed the BglI element to be located approximately 1.6 kb upstream of the 18S gene. The BglI element was used to screen for population-specific markers by Southern analysis. Population-specific banding patterns were only observed in brown trout, allowing identification of individual populations of this species. Sequence comparisons revealed sequences similar to the BglI element present in the rDNA cistron of other salmonids. This result suggests the presence of this sequence in the genome of the salmonid tetraploid ancestor.

Segregation studies and linkage analysis of Atlantic salmon microsatellites using haploid genetics

A genetic marker map of Atlantic salmon would facilitate the identification of loci influencing economically important traits. In the present paper we describe five new Atlantic salmon microsatellites. Segregation studies and linkage analysis of these and previously published microsatellites were carried out in pedigrees consisting of diploid dams and haploid gynogenetic offspring. We confirm earlier reports that salmon microsatellites tend to have a higher number of repeat units than those of mammals. Linkage analysis revealed that three microsatellites belong to a linkage group spanning approximately 50 cM of the genome, whereas the remaining 10 markers seem to be unlinked.

Molecular genetic examination of the polymorphic Arctic charr Salvelinus alpinus of Thingvallavatn, Iceland

Thingvallavatn, Iceland contains two sympatric morphotypes (benthic and limnetic) of Arctic charr Salvelinus alpinus. Each morphotype is composed of two morphs and these differ markedly in ecology, behaviour and life history. We used molecular genetic approaches to test whether (i) genetic heterogeneity exists among morphs and (ii) if morphs arose in allopatry and came into secondary contact or arose sympatrically within the lake through genetic segregation and/or phenotypic plasticity. Direct sequencing of 275 bp of the mitochondrial DNA (mtDNA) control region, mtDNA restriction fragment length polymorphisms and single locus minisatellite analyses detected insufficient variation to test our hypotheses. Analysis of multilocus minisatellite band sharing detected no significant differences between morphs within the same morphotype. However, significant differences among morphs belonging to different morphotypes suggest some genetic heterogeneity in Thingvallavatn charr. Limnetic charr from Thingvallavatn were more similar to sympatric benthic charr than to allopatric limnetics from two other Icelandic lakes. This suggests that the Thingvallavatn morphs arose sympatrically within the lake rather than in allopatry followed by secondary contact.