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

Drywa, Agata; Poćwierz-Kotus, Anita; Was, Anna; Dobosz, Stefan; Kent, Matthew; Lien, Sigbjørn; Bernaś, Rafał; Wenne, Roman

doi:10.1016/j.margen.2012.08.001

Cited by 27 publications

(21 citation statements)

References 62 publications

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“…For comparison, the few studies that used SNPs for evaluating genetic diversity in the S. trutta considered c . 30 markers (Drywa et al ., ; Sušnik Bajec et al ., ). Therefore, this study adds a significant amount of new genomic resources to investigate genetic variation in the S. trutta .…”

Section: Discussionmentioning

confidence: 97%

Genome‐wide nucleotide diversity of hatchery‐rearedAtlantic andMediterranean strains of brown troutSalmo truttacompared to wildMediterranean populations

Leitwein

Gagnaire

Desmarais

et al. 2016

Journal of Fish Biology

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A genome-wide assessment of diversity is provided for wild Mediterranean brown trout Salmo trutta populations from headwater tributaries of the Orb River and from Atlantic and Mediterranean hatchery-reared strains that have been used for stocking. Double-digest restriction-site-associated DNA sequencing (dd-RADseq) was performed and the efficiency of de novo and reference-mapping approaches to obtain individual genotypes was compared. Large numbers of single nucleotide polymorphism (SNP) markers with similar genome-wide distributions were discovered using both approaches (196 639 v. 121 016 SNPs, respectively), with c. 80% of the loci detected de novo being also found with reference mapping, using the Atlantic salmon Salmo salar genome as a reference. Lower mapping density but larger nucleotide diversity (π) was generally observed near extremities of linkage groups, consistent with regions of residual tetrasomic inheritance observed in salmonids. Genome-wide diversity estimates revealed reduced polymorphism in hatchery strains (π = 0·0040 and π = 0·0029 in Atlantic and Mediterranean strains, respectively) compared to wild populations (π = 0·0049), a pattern that was congruent with allelic richness estimated from microsatellite markers. Finally, pronounced heterozygote deficiency was found in hatchery strains (Atlantic F = 0·18; Mediterranean F = 0·42), indicating that stocking practices may affect the genetic diversity in wild populations. These new genomic resources will provide important tools to define better conservation strategies in S. trutta.

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Section: Discussionmentioning

confidence: 97%

Genome‐wide nucleotide diversity of hatchery‐rearedAtlantic andMediterranean strains of brown troutSalmo truttacompared to wildMediterranean populations

Leitwein

Gagnaire

Desmarais

et al. 2016

Journal of Fish Biology

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show abstract

“…An Atlantic salmon derived SNP-array was also used for the genotyping of two populations of Southern Baltic Sea trout S. trutta m. trutta and a diagnostic panel of 39 SNPs was selected for further population genetic analyses and identification of changes related to stocking (Drywa et al, 2013;Pocwierz-Kotus et al, 2014;Wenne et al, 2016b, Wenne et al, 2016c. Large numbers of SNP markers obtained with NGS was used for genome-wide diversity assessment of wild Mediterranean brown trout S. trutta populations and from Atlantic and Mediterranean hatchery-reared strains in southern France that had used for stocking (Leitwein et al, 2016).…”

Section: Comparison Of Wild and Hatchery Stocks: Effects Of Escapeesmentioning

confidence: 99%

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Wenne

2017

Aquat. Living Resour.

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-An increase in aquatic animal production can be achieved by extending aquaculture areas geographically, utilizing new species for culture, and using new technologies. Among new technologies useful for the increase of aquaculture production is the application of genetics and genomics. New molecular tools that benefit aquaculture have been developed. There has been a large number of experimental and review papers published concerning molecular markers and the range of their applications, including aquaculture and food product analyses. Analysis of single nucleotide polymorphisms (SNPs) has emerged as genotyping technology with wide and significant applications in aquaculture. SNPs can be used for construction of genetic linkage maps, finding quantitative trait loci (QTL) for useful traits like growth, body weight, grilsing, thermal and low oxygen tolerance, resistance to stress and diseases, mapping sex determination loci and identification of progeny in selection and chromosome manipulation experiments, assessment of genomic selectionand marker assisted selection in aquaculture. Genome-wide association studies (GWAS) facilitate the finding associations between SNPs and a trait in related or unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genotyping by genome reduction complexity sequencing emerged as an efficient and applicable technology in genomic selection. Identification of genes, sequences and nucleotides (substitutions) directly influencing phenotypic variations opens the possibility of marker-assisted selection for desirable characters in culture. SNP and QTL associations can be enhanced using genome editing technology. Examples of successful applications of SNPs in aquaculture of fish, crustacean and mollusk species, representing most geographic areas, and ecological risks assessment are reviewed.

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“…Assays were designed for 62 candidate SNPs selected from results of genotyping with the Atlantic salmon custom design Illumina iSelect SNP array containing 15 225 markers of 24 samples of sea trout from Vistula and Slupia rivers (Drywa et al 2013;Poćwierz-Kotus et al 2014). SNP genotyping was performed using the Sequenom MassARRAY iPLEX platform (Gabriel et al 2009) in Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway.…”

Section: Snp Genotyping and Evaluation Of Genetic Differences Betweenmentioning

confidence: 99%

“…However, no molecular markers have been found suitable for application in tracing the origin of spawners entering the Vistula river. Newer studies based on SNP methodology enabled the differentiation of the Vistula and Pomeranian (Słupia) sea trout populations (Drywa et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Recent genetic changes in enhanced populations of sea trout (Salmo truttam.trutta) in the southern Baltic rivers revealed with SNP analysis

Wenne

Bernaś

Poćwierz-Kotus

et al. 2016

Aquat. Living Resour.

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-The genetic structure of a fish population is usually thought to be stable over time. In the southern Baltic, Salmo trutta m. trutta (sea trout) populations have been characterized by low degree of genetic differentiation. All studied populations had been heavily stocked with mixed material for many years prior to the sampling period, including releases of Pomeranian sea trout to the Vistula River in Poland, Southern Baltic. However, the strategy of stocking became river based a few years before the sampling began. Juveniles from artificial reproduction are released only to their parental river, which reduces the mixing of the gene pool of fish from different populations. Changes in sea trout populations in the southern Baltic over time were studied using single nucleotide polymorphisms (SNPs). Genetic composition of populations of sea trout in the Vistula and Drwȩca river system were found to increasingly resemble the non-admixed hatchery population from Aquamar (Miastko, Poland), whereas the Pomeranian populations were stable. The implementation of a new stocking strategy for the restoration and protection of Vistula sea trout was noted as possible explanation. With the increase of natural breeding, artificial enhancement of sea trout populations should be reduced.

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

Cited by 27 publications

References 62 publications

Genome‐wide nucleotide diversity of hatchery‐rearedAtlantic andMediterranean strains of brown troutSalmo truttacompared to wildMediterranean populations

Genome‐wide nucleotide diversity of hatchery‐rearedAtlantic andMediterranean strains of brown troutSalmo truttacompared to wildMediterranean populations

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Recent genetic changes in enhanced populations of sea trout (Salmo truttam.trutta) in the southern Baltic rivers revealed with SNP analysis

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