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Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.)

Background: New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wide distributed SNPs enabling genome wide association studies (GWAS). However, genotyping significant numbers of individuals with large number of SNPs remains prohibitively expensive for many research groups. A possible solution to this problem is to determine allele frequencies from pooled DNA samples, such ‘allelotyping’ has been presented as a cost-effective alternative to individual genotyping and has become popular in human GWAS. In this article we have tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon (Salmo salar L.) populations using an Illumina SNP-chip. Results: In total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an Atlantic salmon SNP-chip containing probes for 5568 SNP markers, 3928 of which were bi-allelic. We developed an efficient quality control filter which enables exclusion of loci showing high error rate and minor allele frequency (MAF) close to zero. After applying multiple quality control filters we obtained allele frequency estimates for 3631 bi-allelic loci. We observed high concordance (r > 0.99) between allele frequency estimates derived from individual genotyping and DNA pools. Our results also indicate that even relatively small DNA pools (35 individuals) can provide accurate allele frequency estimates for a given sample. Conclusions: Despite of higher level of variation associated with array replicates compared to pool construction, we suggest that both sources of variation should be taken into account. This study demonstrates that DNA pooling allows fast and high-throughput determination of allele frequencies in Atlantic salmon enabling cost-efficient identification of informative markers for discrimination of populations at various geographical scales, as well as identification of loci controlling ecologically and economically important traitsEuropean Union, Kolarctic ENPI CBC project, Academy of Finland, Norwegian Directorate of Nature Management, Norwegian Research Council, Estonian Science Foundatio

Genetic stock identification of Atlantic salmon and its evaluation in a large population complex

Addressing biocomplexity in fisheries management is a challenge requiring an ability to differentiate among distinct populations contributing to fisheries. We produced extensive genetic baseline data involving 36 sampling locations and 33 microsatellite markers, which allowed characterization of the genetic structure and diversity in a large Atlantic salmon (Salmo salar) population complex of the River Teno system, northernmost Europe. Altogether, we identified 28 hierarchically structured and genetically distinct population segments (global FST = 0.065) corresponding exceptionally well with their geographical locations. An assessment of factors affecting the stock identification accuracy indicated that the identification success is largely defined by the interaction of genetic divergence and the baseline sample sizes. The choice between the two statistical methods tested for performance in genetic stock identification, ONCOR and cBAYES, was not critical, albeit the latter demonstrated slightly higher identification accuracy and lower sensitivity to population composition of the mixture sample. The strong genetic structuring among populations together with a powerful marker system allowed for accurate stock identification of individuals and enabled assessment of stock compositions contributing to mixed-stock fisheries.</p

Chronic diseases and objectively monitored physical activity profile among aged individuals - a cross-sectional twin cohort study

Introduction: High physical activity (PA) at old age indicates good functional capacity enabling independent living. We investigated how different disease conditions are associated with measured PA indicators in old women and men, and whether they recognize this association. Materials and methods: This cross-sectional twin cohort study in Finland comprised 779 individuals (276 complete twin pairs, including 117 monozygotic pairs), who participated in hip-worn accelerometer monitoring of PA and responded to questions on diseases and mobility limitations at mean age of 73 (range 71-75). Results: Of the participants, 23.2% reported having a disease restricting mobility. With sex and age in the regression model, the reported disease restricting mobility explained 11.8% of the variation in moderate-to-vigorous PA (MVPA) and 10.4% of the variation in daily steps. Adding stepwise other self-reported diseases and body mass index to the model increased the explanatory power for MVPA up to 18.5% and 25.5%, and for daily steps up to 16.0% and 20.7%, respectively. In the co-twin control analysis the PA differences were smaller in disease-discordant monozygotic than dizygotic pairs. Conclusions: Chronic disease conditions are associated with low PA, which individuals may not always recognize. Shared genetic factors may explain part of the associations.Key messages Among community-dwelling older men and women one-fourth of the variation in objectively measured moderate-to-vigorous physical activity is accounted for by age, sex, body mass index and self-reported diseases. Occurrence of chronic diseases is associated with low physical activity and individuals do not always recognize this. Healthcare professionals should pay attention to the low physical activity and mobility of individuals with chronic disease conditions before these result in limitations in independent living.Peer reviewe

Chronic diseases and objectively monitored physical activity profile among aged individuals – a cross-sectional twin cohort study

Introduction: High physical activity (PA) at old age indicates good functional capacity enabling independent living. We investigated how different disease conditions are associated with measured PA indicators in old women and men, and whether they recognize this association.Materials and methods: This cross-sectional twin cohort study in Finland comprised 779 individuals (276 complete twin pairs, including 117 monozygotic pairs), who participated in hip-worn accelerometer monitoring of PA and responded to questions on diseases and mobility limitations at mean age of 73 (range 71–75).Results: Of the participants, 23.2% reported having a disease restricting mobility. With sex and age in the regression model, the reported disease restricting mobility explained 11.8% of the variation in moderate-to-vigorous PA (MVPA) and 10.4% of the variation in daily steps. Adding stepwise other self-reported diseases and body mass index to the model increased the explanatory power for MVPA up to 18.5% and 25.5%, and for daily steps up to 16.0% and 20.7%, respectively. In the co-twin control analysis the PA differences were smaller in disease-discordant monozygotic than dizygotic pairs.Conclusions: Chronic disease conditions are associated with low PA, which individuals may not always recognize. Shared genetic factors may explain part of the associations.</p

Long-term leisure-time physical activity and other health habits as predictors of objectively monitored late-life physical activity - A 40-year twin study

Moderate-to-vigorous physical activity (MVPA) in old age is an important indicator of good health and functional capacity enabling independent living. In our prospective twin cohort study with 616 individuals we investigated whether long-term physical activity assessed three times, in 1975, 1982 and 1990 (mean age 48 years in 1990), and other self-reported health habits predict objectively measured MVPA measured with a hip-worn triaxial accelerometer (at least 10 hours per day for at least 4 days) 25 years later (mean age of 73 years). Low leisure-time physical activity at younger age, higher relative weight, smoking, low socioeconomic status, and health problems predicted low MVPA in old age in individual-based analyses (altogether explaining 20.3% of the variation in MVPA). However, quantitative trait modeling indicated that shared genetic factors explained 82% of the correlation between baseline and follow-up physical activity. Pairwise analyses within monozygotic twin pairs showed that only baseline smoking was a statistically significant predictor of later-life MVPA. The results imply that younger-age physical activity is associated with later-life MVPA, but shared genetic factors underlies this association. Of the other predictors mid-life smoking predicted less physical activity at older age independent of genetic factors

A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.)

Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon