Anita Poćwierz-Kotus

Genotyping of two populations of Southern Baltic Sea trout Salmo trutta m. trutta using an Atlantic salmon derived SNP-array.

The sea trout (Salmo trutta m. trutta) is an anadromous, teleost fish species characterized by homing behaviour. The sea trout has considerable ecological and economic significance. It reproduces naturally in rivers flowing into, and is common in, the Baltic Sea. In Poland spawning aggregations occur in the Vistula River and the rivers of Pomerania. Two populations from the Vistula River (TW) and a Pomeranian river, the Słupia (TP) were mixed in the past by stocking. The main purpose of this study was an assessment of the applicability of the Atlantic salmon custom design Illumina iSelect SNP (Single Nucleotide Polymorphisms) array containing 15,225 markers for identification of genetic diversity between sea trout populations. A diagnostic panel of 39 SNPs with a mean FST=0.1298 was selected from a pool of 15,225. At each locus, minor allele frequency was higher than 0.01 and mean expected heterozygosity for TW and TP populations were 0.343 and 0.271 respectively. Individuals tested were clustered in one of two groups which corresponded to their origins where the TW population was genetically more homogenous (membership coefficients ranked from 88.8% to 98.6%) while the TP population was more diverse (membership coefficients ranked from 53.8% to 98.5%). The results demonstrated the applicability of the Salmon 15K SNP-chip for determining the differences between Southern Baltic populations of the sea trout, a closely related salmonid species.

Genetic differentiation of southeast Baltic populations of sea trout inferred from single nucleotide polymorphisms

Sea trout (Salmo trutta m. trutta) is a migratory form of brown trout common in the Baltic Sea. Nine populations from the southeast Baltic (Poland; Lithuania; Denmark, Bornholm; Estonia and Russia) were genotyped using iPLEX Gold technology (Sequenom) with 62 informative SNPs. A diagnostic panel of 23 SNPs was applied to estimate genetic differentiation and assess the population structure of Baltic sea trout. The highest level of pairwise FST differences was observed between the Russian (East Gulf of Finland) and Polish (Baltic main basin) populations. The lowest differences were between the two Polish and the Polish and Lithuanian populations. A genetic similarity was noted between the Estonian Riguldi River and Danish Bornholm populations, and this finding was supported by a Bayesian and factorial correspondence analysis. Diversity within populations was highest for populations from Estonia and lowest for the Lithuanian population. Genetic structure analysis indicated that individuals from the nine populations were clustered into four groups.

Identification of multiple diagnostic SNP loci for differentiation of three salmonid species using SNP-arrays.

This paper reports the use of SNP-array technology in a cross-species study for non-ambiguous species identifications. Based on an existing SNP-array for Atlantic salmon (cross)hybridisations with samples of salmon, brown trout and rainbow trout were analyzed to identify species-specific diagnostic markers. In total 566 SNP loci were identified to be highly polymorphic across the three salmonid species providing the molecular basement for various monitoring applications in aquaculture and food industries.

Restitution and genetic differentiation of salmon populations in the southern Baltic genotyped with the Atlantic salmon 7K SNP array.

BackgroundNative populations of Atlantic salmon in Poland, from the southern Baltic region, became extinct in the 1980s. Attempts to restitute salmon populations in Poland have been based on a Latvian salmon population from the Daugava river. Releases of hatchery reared smolts started in 1986, but to date, only one population with confirmed natural reproduction has been observed in the Slupia river. Our aim was to investigate the genetic differentiation of salmon populations in the southern Baltic using a 7K SNP (single nucleotide polymorphism) array in order to assess the impact of salmon restitution in Poland.MethodsOne hundred and forty salmon samples were collected from: the Polish Slupia river including wild salmon and individuals from two hatcheries, the Swedish Morrum river and the Lithuanian Neman river. All samples were genotyped using an Atlantic salmon 7K SNP array. A set of 3218 diagnostic SNPs was used for genetic analyses.ResultsGenetic structure analyses indicated that the individuals from the investigated populations were clustered into three groups i.e. one clade that included individuals from both hatcheries and the wild population from the Polish Slupia river, which was clearly separated from the other clades. An assignment test showed that there were no stray fish from the Morrum or Neman rivers in the sample analyzed from the Slupia river. Global FST over polymorphic loci was high (0.177). A strong genetic differentiation was observed between the Lithuanian and Swedish populations (FST = 0.28).ConclusionsWild juvenile salmon specimens that were sampled from the Slupia river were the progeny of fish released from hatcheries and, most likely, were not progeny of stray fish from Sweden or Lithuania. Strong genetic differences were observed between the salmon populations from the three studied locations. Our recommendation is that future stocking activities that aim at restituting salmon populations in Poland include stocking material from the Lithuanian Neman river because of its closer geographic proximity.

The genetic relationship between extirpated and contemporary Atlantic salmon Salmo salar L. lines from the southern Baltic Sea

BackgroundThe genetic relationship between original Atlantic salmon populations that are now extinct in the southern Baltic Sea and the present-day populations has long been controversial. To investigate and clarify this issue, we successfully genotyped individuals of the historical populations from the Oder and Vistula Rivers using DNA extracted from dried scales with the Atlantic salmon single nucleotide polymorphism array.ResultsOur results showed a global FST of 0.2515 for all pairs of loci, which indicates a high level of genetic differentiation among the groups analyzed in this study. Pairwise FST values were significant for all comparisons and the highest values were found between present-day reintroduced Slupia River salmon and extinct Vistula River Atlantic salmon. Bayesian analysis of genetic structure revealed the existence of substructures in the extirpated Polish populations and three main clades among studied stocks.ConclusionsThe historical salmon population from the Oder River was genetically closer to present-day salmon from the Neman River than to the historical salmon from the Vistula River. Vistula salmon clearly separated from all other analyzed salmon stocks. It is likely that the origins of the Atlantic salmon population from the Morrum River and the Polish historical native populations are different.

The application of microarray technology to the identification of Tc1-like element sequences in fish genomes

Abstract The phylogenetic relationships between Tc1 transposable elements have previously been reported for the genomes of some fish species. However, research in this field has been hindered by the low number of fish genome sequences available in databases. The application of a DNA microarray as a universal tool for Tc1 transposon sequence analysis in fish genomes is described here. A prototype oligonucleotide microarray was constructed and used to compare samples of genomic DNA isolated from selected fish species. These results, combined with earlier reported molecular analysis of Tc1 showed the usefulness of DNA microarray in the screening of transposon sequences.

Identification of a Tc1-like transposon integration site in the genome of the flounder (Platichthys flesus): a novel use of an inverse PCR method.

The inverse PCR method has been developed and applied employed for the identification of the integration sites of the Tc1-like transposons in the genome of the flounder, Platichthys flesus. One Tc1-like insertion instance was recognized and characterized, demonstrating an efficiency of the method for determining of transposon integration sites. The similarity of the sequence flanking transposon (SFT) to reverse transcriptase sequences (RVT) was demonstrated. It is likely that the insertion took place within currently degenerated LINE (long interspersed nuclear elements) retrotransposon.