An extended panel of single nucleotide polymorphisms in Atlantic salmon (Salmo salar L.) mitochondrial DNA

Karlsson, Sten; Moen, Thomas; Hindar, Kjetil

doi:10.1007/s10592-009-9910-4

Cited by 7 publications

(9 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Ninety-six SNPs (Bourret et al, 2013) were genotyped with an EP1™ 96.96 Dynamic array IFCs (Fluidigm, San Francisco, CA, USA). Fifteen of these SNPs were located in the mitochondrial genome (Karlsson, Moen, & Hindar, 2010).…”

Section: Genotyping and Parental Assignmentmentioning

confidence: 99%

Can variation in standard metabolic rate explain context‐dependent performance of farmed Atlantic salmon offspring?

Robertsen

Reid

Einum

et al. 2018

Ecology and Evolution

Self Cite

View full text Add to dashboard Cite

Escaped farmed Atlantic salmon interbreed with wild Atlantic salmon, leaving offspring that often have lower success in nature than pure wild salmon. On top of this, presence of farmed salmon descendants can impair production of wild‐type recruits. We hypothesize that both these effects connect with farmed salmon having acquired higher standard metabolic rates (SMR, the energetic cost of self‐maintenance) during domestication. Fitness‐related advantages of phenotypic traits associated with both high SMR and farmed salmon (e.g., social dominance) depend on environmental conditions, such as food availability. We hypothesize that farmed offspring have an advantage at high food availability due to, for example, dominance behavior but suffer increased risks of starvation when food is scarce because this behavior is energy‐demanding. To test these hypotheses, we first compare embryo SMR of pure farmed, farmed‐wild hybrids and pure wild offspring. Next, we test early‐life performance (in terms of survival and growth) of hybrids relative to that of their wild half‐siblings, as well as their competitive abilities, in semi‐natural conditions of high and low food availability. Finally, we test how SMR affects early‐life performance at high and low food availability. We find inconclusive support for the hypothesis that domestication has induced increased SMR. Further, wild and hybrid juveniles had similar survival and growth in the semi‐natural streams. Yet, the presence of hybrids led to decreased survival of their wild half‐siblings. Contrary to our hypothesis about context‐dependency, these effects were not modified by food availability. However, wild juveniles with high SMR had decreased survival when food was scarce, but there was no such effect at high food availability. This study provides further proof that farmed salmon introgression may compromise the viability of wild salmon populations. We cannot, however, conclude that this is connected to alterations in the metabolic phenotype of farmed salmon.

show abstract

Section: Genotyping and Parental Assignmentmentioning

confidence: 99%

Can variation in standard metabolic rate explain context‐dependent performance of farmed Atlantic salmon offspring?

Robertsen

Reid

Einum

et al. 2018

Ecology and Evolution

Self Cite

View full text Add to dashboard Cite

show abstract

“…) and 63 SNPs detected by mitochondrial DNA resequencing (Karlsson et al . ). More details regarding the array development strategy and SNP discovery can be found in supplementary methods (Appendix S1).…”

Section: Methodsmentioning

confidence: 97%

SNP‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)

et al. 2012

Self Cite

View full text Add to dashboard Cite

Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this study, we describe the development of a medium-density Atlantic salmon single nucleotide polymorphism (SNP) array based on expressed sequence tags (ESTs) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others. We also discuss the potential future applications of the SNP array for conservation, management and aquaculture.

show abstract

“…Between 28 and 62 specimens per sample were assayed for 19 SNPs in mtDNA (for details see Table 1), as described in Karlsson et al (2009). The 19 SNPs are located in the 12S, ND1, ND2, ND3, ND4, ND5, and ND6 regions of the mtDNA.…”

Section: Mtdna Snp Assaymentioning

confidence: 99%

“…To test these hypotheses we used SNP and microsatellite markers to estimate levels of genetic variability in breeding populations of Atlantic salmon in their 7th generation with levels of genetic variability in wild populations. The SNP markers comprised a newly developed assay including 19 single nucleotide polymorphisms within seven different regions of the mtDNA (Karlsson et al 2009). In a conservation genetics context, two problems are addressed by this study; first, how the formation and maintenance of domesticated populations (but also populations bred in captivity) affect genetic variation at mitochondrial and nuclear loci, and secondly, what consequences escapes of domesticated individuals might have on the genetic variability in wild populations.…”

Section: Introductionmentioning

confidence: 99%

Contrasting patterns of gene diversity between microsatellites and mitochondrial SNPs in farm and wild Atlantic salmon

2010

Self Cite

View full text Add to dashboard Cite

Levels of genetic variability at 12 microsatellite loci and 19 single nucleotide polymorphisms in mitochondrial DNA were studied in four farm strains and four wild populations of Atlantic salmon. Within populations, the farm strains showed significantly lower allelic richness and expected heterozygosity than wild populations at the 12 microsatellite loci, but a significantly higher genetic variability with respect to observed number of haplotypes and haplotype diversity in mtDNA. Significant differences in allele-and haplotype-frequencies were observed between farm strains and wild populations, as well as between different farm strains and between different wild populations. The large genetic differentiation at mitochondrial DNA between wild populations (F ST = 0.24), suggests that the farm strains attained a high mitochondrial genetic variability when created from different wild populations seven generations ago. A large proportion of this variability remains despite an expected lower effective population size for mitochondrial than nuclear DNA. This is best explained by the particular mating schemes in the breeding programmes, with 2-4 females per male. Our observations suggest that for some genetic polymorphisms farm populations might currently hold equal or higher genetic variability than wild populations, but lower overall genetic variability. In the short-term, genetic interactions between escaped farm salmon and wild salmon might increase genetic variability in wild populations, for some, but not most, genetic polymorphisms. In the long term, further losses of genetic variability in farm populations are expected for all genetic polymorphisms, and genetic variability in wild populations will be reduced if escapes of farm salmon continue.

show abstract

An extended panel of single nucleotide polymorphisms in Atlantic salmon (Salmo salar L.) mitochondrial DNA

Cited by 7 publications

References 8 publications

Can variation in standard metabolic rate explain context‐dependent performance of farmed Atlantic salmon offspring?

Can variation in standard metabolic rate explain context‐dependent performance of farmed Atlantic salmon offspring?

SNP‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)

Contrasting patterns of gene diversity between microsatellites and mitochondrial SNPs in farm and wild Atlantic salmon

Contact Info

Product

Resources

About