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

A global synthesis of peer‐reviewed research on the effects of hatchery salmonids on wild salmonids DOI Creative Commons
John McMillan,

Brian P. Morrison,

Nick Chambers

et al.

Fisheries Management and Ecology, Journal Year: 2023, Volume and Issue: 30(5), P. 446 - 463

Published: July 12, 2023

Abstract Hatcheries have long produced salmonids for fisheries and mitigation, though their widespread use is increasingly controversial because of potential impacts to wild salmonids. We conducted a global literature search peer‐reviewed publications (1970–2021) evaluating how hatchery affected salmonids, developed publicly available database, synthesized results. Two hundred six met our criteria, with 83% reporting adverse/minimally adverse effects on Adverse genetic diversity were most common, followed by productivity abundance via ecological processes. Few (3%) reported beneficial nearly all from intensive recovery programs used bolster highly depleted populations. Our review suggests hatcheries commonly in freshwater marine environments. Future research less studied effects—such as epigenetics—could improve knowledge management the full extent impacts.

Language: Английский

Citations

36
Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha DOI Creative Commons

Natasha S. Howe,

Matthew C. Hale, Charles D. Waters

et al.

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(2)

Published: Feb. 1, 2024

Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish subject differential selection pressures compared their counterparts. Domestication selection, or adaptation the environment, poses a risk populations if traits specific success in environment have genetic component there is subsequent introgression between fish. Few studies investigated domestication on genomic level, even fewer done so parallel across multiple hatchery-wild population pairs. In this study, we low-coverage whole-genome sequencing investigate signals of three separate Chinook salmon,

Language: Английский

Citations

10
Environmental epigenetics: Exploring phenotypic plasticity and transgenerational adaptation in fish DOI
Sameh A. Abdelnour, Mohammed A. E. Naiel, Mourad Ben Saïd

et al.

Environmental Research, Journal Year: 2024, Volume and Issue: 252, P. 118799 - 118799

Published: March 27, 2024

Language: Английский

Citations

8
Fish Genomics and Its Application in Disease‐Resistance Breeding DOI Creative Commons
Yu Huang, Zeyu Li,

Mengcheng Li

et al.

Reviews in Aquaculture, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 10, 2024

ABSTRACT Global aquaculture production has been rising for several decades, with up to 76% of the total from fish. However, problem fish diseases is becoming more and prominent in today's context pursuing sustainable aquaculture. Since first genome assembly reported 2002, genomic approaches have successfully implemented breeding enhance disease resistance reduce economic losses caused by diverse diseases. Here, we present a review current progress genomics its application disease‐resistance breeding. First, data all publicly available genomes were curated statistical analysis these performed. Subsequently, genomics‐assisted (including quantitative trait loci mapping, genome‐wide association study, marker‐assisted selection, gene transfer, editing) that applied practical disease–resistance programs are outlined. In addition, candidate genetic markers could possibly be utilized summarized. Finally, remaining challenges further directions discussed. summary, this provides insight into disease‐resistant varieties.

Language: Английский

Citations

8
Microplastic exposure is associated with epigenomic effects in the model organism Pimephales promelas (fathead minnow) DOI Creative Commons
M. Wade, Kennedy Bucci, Chelsea M. Rochman

et al.

Journal of Heredity, Journal Year: 2024, Volume and Issue: unknown

Published: May 13, 2024

Microplastics have evolutionary and ecological impacts across species, affecting organisms' development, reproduction, behavior along with contributing to genotoxicity stress. As plastic pollution is increasing ubiquitous, gaining a better understanding of organismal responses microplastics necessary. Epigenetic processes such as DNA methylation are heritable forms molecular regulation influenced by environmental conditions. Therefore, determining epigenetic will reveal potential chronic consequences this pollutant. We performed an experiment two generations fathead minnows (Pimephales promelas) elucidate transgenerational effects microplastic exposure. exposed the first generation fish four different treatments microplastics: concentrations each pre-consumer polyethylene (PE) PE collected from Lake Ontario. then raised filial no used enzymatic sequencing on adult liver tissue homogenized larvae evaluate differences among treatments, sexes, generations. Our findings show origin had larger effect in female whereas concentration was stronger males. also observed effects, highlighting mechanism which parents can pass exposure their offspring. Many genes found within differentially methylated regions our analyses known interact estrogenic chemicals associated related metabolism. This study highlights persistent potentially serious gene freshwater systems.

Language: Английский

Citations

4
Endangered Fish Management DOI

Douglas Tave

Published: Jan. 1, 2025

Citations

0
Epigentics DOI

Douglas Tave

Published: Jan. 1, 2025

Citations

0
The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids DOI Creative Commons
Samuel A. May, Samuel W. Rosenbaum, Devon E. Pearse

et al.

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: April 18, 2025

ABSTRACT The increasing feasibility of whole‐genome sequencing has been highly anticipated, promising to transform our understanding the biology nonmodel species. Notably, dramatic cost reductions beginning around 2007 with advent high‐throughput inspired publications heralding ‘genomics revolution’, predictions about its future impacts. Although such served as useful guideposts, value is added when statements are evaluated benefit hindsight. Here, we review 10 key made early in genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on concerning applied aspects and examples involving salmonid species which, due their socioeconomic ecological significance, have frontrunners applications Predicted outcomes included enhanced analytical power, deeper insights into genetic basis phenotype fitness variation, disease management breeding program advancements. many materialised, several expectations remain unmet technological, knowledge barriers. Additionally, largely unforeseen advancements, including identification applicability large‐effect loci, close‐kin mark–recapture, environmental DNA gene editing under‐anticipated value. Finally, emerging innovations artificial intelligence bioinformatics offer new directions. This retrospective evaluation impacts genomic revolution offers for

Language: Английский

Citations

0
Epigenetic Modulations for Prevention of Infectious Diseases in Shrimp Aquaculture DOI Open Access
Gunasekara Chathura Wikumpriya,

Madhuranga Walawedurage Srinith Prabhatha,

Jiye Lee

et al.

Genes, Journal Year: 2023, Volume and Issue: 14(9), P. 1682 - 1682

Published: Aug. 25, 2023

Aquaculture assumes a pivotal role in meeting the escalating global food demand, and shrimp farming, particular, holds significant economy security, providing rich source of nutrients for human consumption. Nonetheless, industry faces formidable challenges, primarily attributed to disease outbreaks diminishing efficacy conventional management approaches, such as antibiotic usage. Consequently, there is an urgent imperative explore alternative strategies ensure sustainability industry. In this context, field epigenetics emerges promising avenue combating infectious diseases aquaculture. Epigenetic modulations entail chemical alterations DNA proteins, orchestrating gene expression patterns without modifying underlying sequence through methylation, histone modifications, non-coding RNA molecules. Utilizing epigenetic mechanisms presents opportunity enhance immune bolster resistance shrimp, thereby contributing optimizing health productivity. Additionally, concept inheritability marine animals immense potential future farming To end, comprehensive review thoroughly explores dynamics aquaculture, with particular emphasis on its management. It conveys significance harnessing advantageous changes long-term viability while deliberating consequences these interventions. Overall, appraisal highlights trajectory applications, propelling toward strengthening

Language: Английский

Citations

9
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.

Evolution, Journal Year: 2024, Volume and Issue: 78(8), P. 1441 - 1452

Published: May 13, 2024

Abstract Large effect loci often contain genes with critical developmental functions and potentially broad effects across life stages. However, their stage-specific fitness consequences are rarely explored. In Atlantic salmon, variation in two large-effect loci, six6 vgll3, is linked to age at maturity several physiological behavioral traits early life. By genotyping the progeny of wild salmon that were planted into natural streams nutrient manipulations, we tested if genetic these associated survival We found higher early-life was genotype late maturation but locus. These significant high nutrients not low-nutrient streams. The differences explained by additive offspring generation maternal genotypes locus both parents’ vgll3 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

2