Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon (Salmo salar) and other salmonid fishes

BACKGROUND: Single nucleotide polymorphisms (SNPs) represent the most abundant type of DNA variation in the vertebrate genome, and their applications as genetic markers in numerous studies of molecular ecology and conservation of natural populations are emerging. Recent large-scale sequencing projects in several fish species have provided a vast amount of data in public databases, which can be utilized in novel SNP discovery in salmonids. However, the suggested duplicated nature of the salmonid genome may hamper SNP characterization if the primers designed in conserved gene regions amplify multiple loci. RESULTS: Here we introduce a new intron-primed exon-crossing (IPEC) method in an attempt to overcome this duplication problem, and also evaluate different priming methods for SNP discovery in Atlantic salmon (Salmo salar) and other salmonids. A total of 69 loci with differing priming strategies were screened in S. salar, and 27 of these produced ~13 kb of high-quality sequence data consisting of 19 SNPs or indels (one per 680 bp). The SNP frequency and the overall nucleotide diversity (3.99 × 10(-4)) in S. salar was lower than reported in a majority of other organisms, which may suggest a relative young population history for Atlantic salmon. A subset of primers used in cross-species analyses revealed considerable variation in the SNP frequencies and nucleotide diversities in other salmonids. CONCLUSION: Sequencing success was significantly higher with the new IPEC primers; thus the total number of loci to screen in order to identify one potential polymorphic site was six times less with this new strategy. Given that duplication may hamper SNP discovery in some species, the IPEC method reported here is an alternative way of identifying novel polymorphisms in such cases

Genetic growth potential, rather than phenotypic size, predicts migration phenotype in Atlantic salmon

Knowledge of the relative importance of genetic versus environmental determinants of major developmental transitions is pertinent to understanding phenotypic evolution. In salmonid fishes, a major developmental transition enables a risky seaward migration that provides access to feed resources. In Atlantic salmon, initiation of the migrant phenotype, and thus age of migrants, is presumably controlled via thresholds of a quantitative liability, approximated by body size expressed long before the migration. However, how well size approximates liability, both genetically and environmentally, remains uncertain. We studied 32 Atlantic salmon families in two temperatures and feeding regimes (fully fed, temporarily restricted) to completion of migration status at age 1 year. We detected a lower migrant probability in the cold (0.42) than the warm environment (0.76), but no effects of male maturation status or feed restriction. By contrast, body length in late summer predicted migrant probability and its control reduced migrant probability heritability by 50-70%. Furthermore, migrant probability and length showed high heritabilities and between-environment genetic correlations, and were phenotypically highly correlated with stronger genetic than environmental contributions. Altogether, quantitative estimates for the genetic and environmental effects predicting the migrant phenotype indicate, for a given temperature, a larger importance of genetic than environmental size effects.Peer reviewe

Cross-species amplification of 36 cyprinid microsatellite loci in Phoxinus phoxinus (L.) and Scardinius erythrophthalmus (L.)

<p>Abstract</p> <p>Background</p> <p>To conduct phylogeographic or population genetic studies, an adequate number of DNA markers for the focal species are required. Due to severe unavailability of genotype markers of any kind for the species Eurasian minnow (<it>Phoxinus phoxinus </it>L.) and rudd (<it>Scardinius erythrophthalmus </it>L.), we set out to attempt cross-amplification of a set of microsatellite loci from related species.</p> <p>Findings</p> <p>We tested 36 cyprinid microsatellite loci for cross-species amplification in minnow and rudd. Fifteen species-locus combinations produced amplifications in minnow, seven being polymorphic, while 18 combinations amplified in rudd, nine of these being polymorphic.</p> <p>Conclusions</p> <p>The positive cross-species amplifications present potential contributions to the establishment of genetic marker sets for population genetics studies of the two focal species.</p

Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon

<p>Abstract</p> <p>Background</p> <p>For decades, linkage mapping has been one of the most powerful and widely used approaches for elucidating the genetic architecture of phenotypic traits of medical, agricultural and evolutionary importance. However, successful mapping of Mendelian and quantitative phenotypic traits depends critically on the availability of fast and preferably high-throughput genotyping platforms. Several array-based single nucleotide polymorphism (SNP) genotyping platforms have been developed for genetic model organisms during recent years but most of these methods become prohibitively expensive for screening large numbers of individuals. Therefore, inexpensive, simple and flexible genotyping solutions that enable rapid screening of intermediate numbers of loci (~75-300) in hundreds to thousands of individuals are still needed for QTL mapping applications in a broad range of organisms.</p> <p>Results</p> <p>Here we describe the discovery of and application of insertion-deletion (INDEL) polymorphisms for cost-efficient medium throughput genotyping that enables analysis of >75 loci in a single automated sequencer electrophoresis column with standard laboratory equipment. Genotyping of INDELs requires low start-up costs, includes few standard sample handling steps and is applicable to a broad range of species for which expressed sequence tag (EST) collections are available. As a proof of principle, we generated a partial INDEL linkage map in Atlantic salmon (<it>Salmo salar</it>) and rapidly identified a number of quantitative trait loci (QTLs) affecting early life-history traits that are expected to have important fitness consequences in the natural environment.</p> <p>Conclusions</p> <p>The INDEL genotyping enabled fast coarse-mapping of chromosomal regions containing QTL, thus providing an efficient means for characterization of genetic architecture in multiple crosses and large pedigrees. This enables not only the discovery of larger number of QTLs with relatively smaller phenotypic effect but also provides a cost-effective means for evaluation of the frequency of segregating QTLs in outbred populations which is important for further understanding how genetic variation underlying phenotypic traits is maintained in the wild.</p

Standard metabolic rate does not associate with age-at-maturity genotype in juvenile Atlantic salmon

Atlantic salmon (Salmo salar) is a species with diverse life-history strategies, to which the timing of maturation contributes considerably. Recently, the genome region including the gene vgll3 has gained attention as a locus with a large effect on Atlantic salmon maturation timing, and recent studies on the vgll3 locus in salmon have indicated that its effect might be mediated through body condition and accumulation of adipose tissue. However, the cellular and physiological pathways leading from vgll3 genotype to phenotype are still unknown. Standard metabolic rate is a potentially important trait for resource acquisition and assimilation and we hypothesized that this trait, being a proxy for the maintenance energy expenditure of an individual, could be an important link in the pathway from vgll3 genotype to maturation timing phenotype. As a first step to studying links between vgll3 and the metabolic phenotype of Atlantic salmon, we measured the standard metabolic rate of 150 first-year Atlantic salmon juveniles of both sexes, originating from 14 different families with either late-maturing or early-maturing vgll3 genotypes. No significant difference in mass-adjusted standard metabolic rate was detected between individuals with different vgll3 genotypes, indicating that juvenile salmon of different vgll3 genotypes have similar maintenance energy requirements in the experimental conditions used and that the effects of vgll3 on body condition and maturation are not strongly related to maintenance energy expenditure in either sex at this life stage.Peer reviewe

Unanticipated population structure of European grayling in its northern distribution: implications for conservation prioritization

<p>Abstract</p> <p>Background</p> <p>The European grayling (<it>Thymallus thymallus</it>) is a salmonid fish native to Europe, with a distribution ranging from England and France to the Ural Mountains of north-western Russia. The majority of grayling populations inhabit freshwater rivers and lakes but some populations also occupy brackish water in northern parts of the Baltic Sea. Previous population genetic studies have demonstrated that grayling populations in Finland, Estonia and Russia belong to a single mitochondrial lineage and exhibit high levels of differentiation even at a small geographic scale. As a result, we predicted that grayling populations should not cluster regionally. Despite the extensive amount of genetic research that has been carried out on grayling, comprehensive national-level information on population structure of grayling in Northern Europe is still lacking. Yet this is the level at which populations are currently managed.</p> <p>Results</p> <p>We found unanticipated population structure of grayling clustering into three groups largely corresponding to the northern, Baltic and south-eastern geographic areas of Finland using 13 microsatellite loci. We also found a high level of genetic differentiation among the groups and moderate to high differentiation within the groups. This combined with low variability strongly indicates that genetic drift and limited migration have a major impact on grayling population structure. An allele size permutation test indicated that mutations at microsatellite loci have not significantly contributed to genetic differentiation among the three Finnish groups. However, at the European scale, mutations had significantly contributed to population differentiation.</p> <p>Conclusion</p> <p>This research provides novel genetic information on European grayling in its northern distribution range and has clear implications for supporting country-scale conservation efforts. Specifically, the strong between population divergence observed indicates that single populations should generally be recognized as separate management units. We also introduced an alternative prioritization strategy for population conservation based on the evaluation of the relative roles of different evolutionary forces shaping the gene pools. We envision that the proposed approach to categorize populations for conservation will be a useful tool for wildlife researchers and conservationists working on a diverse range of organisms.</p

Temporal variation in lake-run brown trout (Salmo trutta) mixed-stock fishery catches in a large Fennoscandian lake

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