Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: sex-specificity and intergenerational stability DOI Creative Commons
Clare J. Venney, Raphaël Bouchard,

Julien April

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Oct. 7, 2022

Abstract Captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness within a single generation, even the absence of genetic change. Evidence for hatchery-induced changes DNA methylation is becoming abundant, though questions remain sex-specificity these effects, their persistence until spawning, potential transmission to future generations. Here we performed whole genome sequencing fin tissue 16 hatchery wild Atlantic ( Salmo salar ) returning spawn Rimouski River, Québec. We identified two cohorts hatchery-reared through analysis, one which was epigenetically similar fish, suggesting that supplementation efforts may be able minimize epigenetic effects rearing. found sex-specific rearing, with few genomic regions being affected males females. also analysed methylome 32 F1 offspring from four groups (pure wild, pure origin, reciprocal hybrids). due parental persisted patterns inheritance appear complex, involving nonadditive effects. Our results suggest minimal F0. There rapid loss associated However, inheritance, captive are rather complex field would benefit further research minimizing conservation efforts.

Language: Английский

Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: Sex‐specificity and intergenerational stability DOI Creative Commons
Clare J. Venney, Raphaël Bouchard,

Julien April

et al.

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 10, 2023

Captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness within a single generation, even the absence of genetic change. Evidence for hatchery-induced changes DNA methylation is becoming abundant, though questions remain sex-specificity these effects, their persistence until spawning potential transmission to future generations. Here we performed whole genome sequencing fin tissue 16 hatchery wild Atlantic (Salmo salar) returning spawn Rimouski River, Québec, Canada. We identified two cohorts hatchery-reared through analysis, one which was epigenetically similar fish, suggesting that supplementation efforts may be able minimize epigenetic effects rearing. found sex-specific rearing, with few genomic regions being affected males females. also analysed methylome 32 F

Language: Английский

Citations

5
Epigenetics in fish evolution DOI
Francesc Piferrer, Eric A. Miska, Dafni Anastasiadi

et al.

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 283 - 306

Published: Jan. 1, 2024

Language: Английский

Citations

1
Single generation epigenetic change in captivity and reinforcement in subsequent generations in a delta smelt (Hypomesus transpacificus) conservation hatchery DOI Creative Commons
Ensieh Habibi, Michael R. Miller, Andrea Schreier

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(15)

Published: July 5, 2024

Abstract A refugial population of the endangered delta smelt ( Hypomesus transpacificus ) has been maintained at Fish Conservation and Culture Laboratory (FCCL) UC Davis since 2008. Despite intense genetic management, fitness differences between wild cultured fish have observed FCCL. To investigate molecular underpinnings hatchery domestication, we used whole‐genome bisulfite sequencing to quantify epigenetic hatchery‐origin smelt. Differentially methylated regions (DMRs) were identified from 104 individuals by comparing methylation patterns in different generations (G1, G2, G3) with their parents (G0). We discovered a total 132 significant DMRs p < .05) G0 G1, 201 G3. Our results demonstrate substantial emerged hatchery‐reared early hatchery, higher proportion hypermethylated fish. The rearing environment was found be stronger predictor individual clustering based on than family, sex or generation. study indicates reinforcement status successive environment, as evidenced an increase decrease hypomethylated over time. Lastly, our demonstrated heterogeneity inherited pattern families across generations. These insights highlight long‐term consequences practices landscape, potentially impacting populations.

Language: Английский

Citations

1
Genomic Signatures of Domestication in European Seabass (Dicentrarchus labrax L.) Reveal a Potential Role for Epigenetic Regulation in Adaptation to Captivity DOI Creative Commons
Aristotelis Moulistanos,

Konstantinos Papasakellariou,

Ioannis Kavakiotis

et al.

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(12)

Published: Dec. 1, 2024

ABSTRACT Genome scans provide a comprehensive method to explore genome‐wide variation associated with traits under study. However, linking individual genes broader functional groupings and pathways is often challenging, yet crucial for understanding the evolutionary mechanisms underlying these traits. This task particularly relevant multi‐trait processes such as domestication, which are influenced by complex interactions between numerous genetic non‐genetic factors, including epigenetic regulation. As various within spectrum of domestication selected in concert over time, this process offers an opportunity identify overlaps understand integrated architecture In study, we analyzed approximately 600,000 SNPs from Pool‐Seq experiment comparing eight natural‐origin 12 farmed populations European seabass Mediterranean Sea region. We implemented two genome scan approaches focused on genomic regions supported both methods, resulting identification 96 candidate genes, nine CpG islands, highligt potential influences. Many islands linkage groups previously domestication‐related The most significantly overrepresented molecular function was “oxidoreductase activity”. Furthermore, dense network identified, connecting 22 genes. Within network, enriched central were involved “chromatin organization”, highlighting another mechanism. Altogether, our findings underscore utility interactome‐assisted pathway analysis elucidating polygenic suggest that regulation may play role seabass.

Language: Английский

Citations

1
The adaptation of rainbow trout to warmer water: Oxidative damage in the germinal line DOI Creative Commons
Vianel Sevastei, Sonia A. Crichigno, María Victoria Santos

et al.

Aquaculture and Fisheries, Journal Year: 2023, Volume and Issue: 10(1), P. 68 - 78

Published: July 29, 2023

Contemporary evolution was observed in a feral rainbow trout (Oncorhynchus mykiss) population of thermal stream (Valcheta) Northern Patagonia, terms juvenile tolerance and preferred temperature. Other authors showed that high-temperature treatment applied to male juveniles increased the next generation. This implies high mutation rate and/or modified epigenetic inheritance. Comparisons were made among a) strain adapted upper higher temperature (Valcheta stream), b) wild temperate (Guillelmo c) two farmed strains. We examined: Oxidative damage (lipid peroxidation) activities antioxidant enzymes; Catalase (CAT), Glutathione S-Transferases (GST), Superoxide Dismutase (SOD), liver, testicle, spermatozoa. Semen fatty acid composition, sperm morphology, motility, fertilization performance samples before after application cryopreservation procedures also evaluated. The responses, mainly related membrane, reinforces idea ROS can affect germinal line subjected water Our results suggest acquired traits may be part wide spectrum novel characteristics produced as consequence an enhanced different DNA methylation pattern, induced by temperatures mediated ROS.

Language: Английский

Citations

1
Early survival in Atlantic salmon is associated with parental genotypes at loci linked to timing of maturation DOI Creative Commons
Tutku Aykanat, Darryl McLennan, Neil B. Metcalfe

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 8, 2024

Abstract Large effects loci often contain genes with critical developmental functions potentially broad across life-stages. However, the life-stage-specific fitness consequences are rarely explored. In Atlantic salmon, variation in two large-effect loci, six6 and vgll3 , is linked to age at maturity, several physiological behavioural traits early life. By genotyping progeny of wild salmon that were planted into natural streams nutrient manipulations, we tested if genetic these associated survival We found higher life was genotype late maturation but locus. These significant high-nutrient, not low-nutrient streams. The differences explained by additive offspring generation, maternal genotypes locus, both parents’ Our results suggest indirect can be determinants fitness. This study demonstrates an intriguing case how exhibit complex associations stages indicates predicting evolutionary dynamics difficult.

Language: Английский

Citations

0
A Review of Factors Affecting Farmed Atlantic Salmon (Salmo salar) Welfare in Australia and Beyond DOI Open Access
Craig A. Layman, Julianna Kadar, Brianne Lyall

et al.

Published: April 11, 2024

With the increasingly global scale and scope of aquaculture, need to match this development with improvements in fish welfare is a central societal industry goal. We provide comprehensive assessment farmed Atlantic salmon (Salmo salar) literature targeted examples focusing on Tasmania, Australia. synthesise insights from both small- industry-scale perspectives, highlighting other reviews that discussions particular sub-areas research. focus recent advances improved methods for handling management, behaviour, health issues breeding. also address wildlife interactions resulting farming, as well future research directions system development. This review can serve basis aquaculture management guidelines place individual primary

Language: Английский

Citations

0
Selection among critically endangered landlocked salmon (Salmo salar m. sebago) families in survival and growth traits across early life stages and in different environments DOI Creative Commons
Matti Janhunen, Aslak Eronen, Jukka Kekäläinen

et al.

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(4)

Published: April 1, 2024

Abstract Endangered wild fish populations are commonly supported by hatchery propagation. However, hatchery‐reared experience very different selective pressures compared to their counterparts, potentially causing genotype‐by‐environment interactions (G × E) in essential fitness traits. We experimentally studied early selection a critically endangered landlocked Atlantic salmon population, first from fertilization the swim‐up stage common setting, and thereafter until age of 5 months two contrasting rearing environments. Swim‐up progeny were moved either standard indoor tanks involving conventional husbandry or seminatural outdoor channels providing only natural food. After summer, sampled survivors assigned families genotyping. Early survival was mostly determined maternal effects, but also involved significant variation due sires full‐sib (potential genetic effects). High on‐growing (88.7%) maintained more even distribution among (relative share 1.5%–4.2%) than environment (0.0%–5.4%). This heterogeneity maternal, whereas no independent paternal effect occurred. Heritability estimates high for body size traits both environments (0.62–0.69). Genetic correlations between significantly positive (0.67–0.69), condition genetically linked rapid growth (0.54). Additive phenotypic increased environment, scaling effects probably played less role G E, re‐ranking genotypes. Our results suggest that not direct according environmental conditions experienced. Consistently implies that, despite its low overall diversity long history captive (>50 years), this population still possesses adaptive potential response change back conditions.

Language: Английский

Citations

0
Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: sex-specificity and intergenerational stability DOI Creative Commons
Clare J. Venney, Raphaël Bouchard,

Julien April

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Oct. 7, 2022

Abstract Captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness within a single generation, even the absence of genetic change. Evidence for hatchery-induced changes DNA methylation is becoming abundant, though questions remain sex-specificity these effects, their persistence until spawning, potential transmission to future generations. Here we performed whole genome sequencing fin tissue 16 hatchery wild Atlantic ( Salmo salar ) returning spawn Rimouski River, Québec. We identified two cohorts hatchery-reared through analysis, one which was epigenetically similar fish, suggesting that supplementation efforts may be able minimize epigenetic effects rearing. found sex-specific rearing, with few genomic regions being affected males females. also analysed methylome 32 F1 offspring from four groups (pure wild, pure origin, reciprocal hybrids). due parental persisted patterns inheritance appear complex, involving nonadditive effects. Our results suggest minimal F0. There rapid loss associated However, inheritance, captive are rather complex field would benefit further research minimizing conservation efforts.

Language: Английский

Citations

2