1
|
Wellband K, Roth D, Linnansaari T, Curry RA, Bernatchez L. Environment-driven reprogramming of gamete DNA methylation occurs during maturation and is transmitted intergenerationally in Atlantic Salmon. G3 (BETHESDA, MD.) 2021; 11:jkab353. [PMID: 34849830 PMCID: PMC8664423 DOI: 10.1093/g3journal/jkab353] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/24/2021] [Indexed: 02/06/2023]
Abstract
An epigenetic basis for transgenerational plasticity in animals is widely theorized, but convincing empirical support is limited by taxa-specific differences in the presence and role of epigenetic mechanisms. In teleost fishes, DNA methylation generally does not undergo extensive reprogramming and has been linked with environmentally induced intergenerational effects, but solely in the context of early life environmental differences. Using whole-genome bisulfite sequencing, we demonstrate that differential methylation of sperm occurs in response to captivity during the maturation of Atlantic Salmon (Salmo salar), a species of major economic and conservation significance. We show that adult captive exposure further induces differential methylation in an F1 generation that is associated with fitness-related phenotypic differences. Some genes targeted with differential methylation were consistent with genes differential methylated in other salmonid fishes experiencing early-life hatchery rearing, as well as genes under selection in domesticated species. Our results support a mechanism of transgenerational plasticity mediated by intergenerational inheritance of DNA methylation acquired late in life for salmon. To our knowledge, this is the first-time environmental variation experienced later in life has been directly demonstrated to influence gamete DNA methylation in fish.
Collapse
Affiliation(s)
- Kyle Wellband
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - David Roth
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Tommi Linnansaari
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - R Allen Curry
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
| |
Collapse
|
2
|
Abass NY, Su B, Alsaqufi A, Elaswad A, Qin Z, Li H, Odin R, Ye Z, Dunham RA. Growth Differences of Growth Hormone Transgenic Female and Male Channel Catfish, Ictalurus punctatus, Grown in Earthen Ponds to Sexual Maturation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:870-880. [PMID: 34595591 DOI: 10.1007/s10126-021-10069-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
This study compared growth performance between female and male transgenic channel catfish, Ictalurus punctatus, containing channel catfish growth hormone full-length cDNA driven by the ocean pout antifreeze protein promoter, opAFP-ccGH, the rainbow trout metallothionein promoter, rtMT-ccGH, or both constructs, and their non-transgenic siblings in earthen ponds at 16 and 48 months of age. Body weight between the transgenic and their non-transgenic siblings differed (P < 0.001) at all ages. Transgenic F2 opAFP-ccGH grew 1.51- to 2.58-, F2 rtMT-ccGH grew 1.44- to 2.99- and F1fish transgenic for both constructs grew 1.36- to 2.92- fold larger than their non-transgenic sibling controls, depending upon age and sex. Body weight of the transgenic GH males was significantly higher than those of the transgenic GH females at 16 months of age (P < 0.001). However, body weight of the transgenic GH females was significantly higher (P < 0.001) compared with those of the transgenic GH males at 48 months of age, but not for the double transgenics (P > 0.05). In the case of non-transgenic GH siblings, males were larger than females at both 16 and 48 months of age (P < 0.001). Sexually dimorphic responses to GH transgenes were the opposite after sexual maturation. When critically low dissolved oxygen levels were encountered, survival of transgenic male and female opAFP-ccGH channel catfish was lower than that of controls (P = 0.004), as well as rtMT-ccGH females (P = 0.11), which is not surprising since the largest fish are most likely to succumb during an oxygen depletion.
Collapse
Affiliation(s)
- Nermeen Y Abass
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
- Department of Agricultural Botany, Faculty of Agriculture Saba-Basha, Alexandria University, P.O. Box 21531, Alexandria, Egypt.
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ahmed Alsaqufi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Department of Aquaculture and Animal Production, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 31982, Al-Ahsa, Saudi Arabia
| | - Ahmed Elaswad
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Zhenkui Qin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Hanbo Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ramjie Odin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Mindanao State University - Maguindanao, Datu Odin Sinsuat, 9601, Maguindanao, Philippines
| | - Zhi Ye
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Rex A Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| |
Collapse
|
3
|
Lalyer CR, Sigsgaard L, Giese B. Ecological vulnerability analysis for suppression of Drosophila suzukii by gene drives. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
4
|
Christensen KA, Le Luyer J, Chan MTT, Rondeau EB, Koop BF, Bernatchez L, Devlin RH. Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon. G3 (BETHESDA, MD.) 2021; 11:jkab021. [PMID: 33712817 PMCID: PMC8022943 DOI: 10.1093/g3journal/jkab021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/13/2021] [Indexed: 12/24/2022]
Abstract
Genotype-by-environment (GxE) interactions are non-parallel reaction norms among individuals with different genotypes in response to different environmental conditions. GxE interactions are an extension of phenotypic plasticity and consequently studying such interactions improves our ability to predict effects of different environments on phenotype as well as the fitness of genetically distinct organisms and their capacity to interact with ecosystems. Growth hormone transgenic coho salmon grow much faster than non-transgenics when raised in tank environments, but show little difference in growth when reared in nature-like streams. We used this model system to evaluate potential mechanisms underlying this growth rate GxE interaction, performing RNA-seq to measure gene transcription and whole-genome bisulfite sequencing to measure gene methylation in liver tissue. Gene ontology (GO) term analysis revealed stress as an important biological process potentially influencing growth rate GxE interactions. While few genes with transcription differences also had methylation differences, in promoter or gene regions, many genes were differentially methylated between tank and stream environments. A GO term analysis of differentially methylated genes between tank and stream environments revealed increased methylation in the stream environment of more than 95% of the differentially methylated genes, many with biological processes unrelated to liver function. The lower nutritional condition of the stream environment may cause increased negative regulation of genes less vital for liver tissue function than when fish are reared in tanks with unlimited food availability. These data show a large effect of rearing environment both on gene expression and methylation, but it is less clear that the detected epigenetic marks are responsible for the observed altered growth and physiological responses.
Collapse
Affiliation(s)
- Kris A Christensen
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Jérémy Le Luyer
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V OA6, Canada
| | - Michelle T T Chan
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
- Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Eric B Rondeau
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V OA6, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
| |
Collapse
|
5
|
Then C, Kawall K, Valenzuela N. Spatiotemporal Controllability and Environmental Risk Assessment of Genetically Engineered Gene Drive Organisms from the Perspective of European Union Genetically Modified Organism Regulation. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2020; 16:555-568. [PMID: 32250054 PMCID: PMC7496464 DOI: 10.1002/ieam.4278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/16/2019] [Accepted: 03/30/2020] [Indexed: 05/12/2023]
Abstract
Gene drive organisms are a recent development created by using methods of genetic engineering; they inherit genetic constructs that are passed on to future generations with a higher probability than with Mendelian inheritance. There are some specific challenges inherent to the environmental risk assessment (ERA) of genetically engineered (GE) gene drive organisms because subsequent generations of these GE organisms might show effects that were not observed or intended in the former generations. Unintended effects can emerge from interaction of the gene drive construct with the heterogeneous genetic background of natural populations and/or be triggered by changing environmental conditions. This is especially relevant in the case of gene drives with invasive characteristics and typically takes dozens of generations to render the desired effect. Under these circumstances, "next generation effects" can substantially increase the spatial and temporal complexity associated with a high level of uncertainty in ERA. To deal with these problems, we suggest the introduction of a new additional step in the ERA of GE gene drive organisms that takes 3 criteria into account: the biology of the target organisms, their naturally occurring interactions with the environment (biotic and abiotic), and their intended biological characteristics introduced by genetic engineering. These 3 criteria are merged to form an additional step in ERA, combining specific "knowns" and integrating areas of "known unknowns" and uncertainties, with the aim of assessing the spatiotemporal controllability of GE gene drive organisms. The establishment of assessing spatiotemporal controllability can be used to define so-called "cut-off criteria" in the risk analysis of GE gene drive organisms: If it is likely that GE gene drive organisms escape spatiotemporal controllability, the risk assessment cannot be sufficiently reliable because it is not conclusive. Under such circumstances, the environmental release of the GE gene drive organisms would not be compatible with the precautionary principle (PP). Integr Environ Assess Manag 2020;16:555-568. © 2020 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
Collapse
Affiliation(s)
- Christoph Then
- Testbiotech e.V., Institute for Independent Impact Assessment of BiotechnologyMunichGermany
| | | | - Nina Valenzuela
- Testbiotech e.V., Institute for Independent Impact Assessment of BiotechnologyMunichGermany
| |
Collapse
|
6
|
Devos Y, Craig W, Devlin RH, Ippolito A, Leggatt RA, Romeis J, Shaw R, Svendsen C, Topping CJ. Using problem formulation for fit-for-purpose pre-market environmental risk assessments of regulated stressors. EFSA J 2019; 17:e170708. [PMID: 32626445 PMCID: PMC7055725 DOI: 10.2903/j.efsa.2019.e170708] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Pre-market/prospective environmental risk assessments (ERAs) contribute to risk analyses performed to facilitate decisions about the market introduction of regulated stressors. Robust ERAs begin with an explicit problem formulation, which involves among other steps: (1) formally devising plausible pathways to harm that describe how the deployment of a regulated stressor could be harmful; (2) formulating risk hypotheses about the likelihood and severity of such events; (3) identifying the information that will be useful to test the risk hypotheses; and (4) developing a plan to acquire new data for hypothesis testing should tests with existing information be insufficient for decision-making. Here, we apply problem formulation to the assessment of possible adverse effects of RNA interference-based insecticidal genetically modified (GM) plants, GM growth hormone coho salmon, gene drive-modified mosquitoes and classical biological weed control agents on non-target organisms in a prospective manner, and of neonicotinoid insecticides on bees in a retrospective manner. In addition, specific considerations for the problem formulation for the ERA of nanomaterials and for landscape-scale population-level ERAs are given. We argue that applying problem formulation to ERA maximises the usefulness of ERA studies for decision-making, through an iterative process, because: (1) harm is defined explicitly from the start; (2) the construction of risk hypotheses is guided by policy rather than an exhaustive attempt to address any possible differences; (3) existing information is used effectively; (4) new data are collected with a clear purpose; (5) risk is characterised against well-defined criteria of hypothesis corroboration or falsification; and (6) risk assessment conclusions can be communicated clearly. However, problem formulation is still often hindered by the absence of clear policy goals and decision-making criteria (e.g. definition of protection goals and what constitutes harm) that are needed to guide the interpretation of scientific information. We therefore advocate further dialogue between risk assessors and risk managers to clarify how ERAs can address policy goals and decision-making criteria. Ideally, this dialogue should take place for all classes of regulated stressors, as this can promote alignment and consistency on the desired level of protection and maximum tolerable impacts across regulated stressors.
Collapse
Affiliation(s)
- Yann Devos
- GMO Unit European Food Safety Authority (EFSA) Italy
| | - Wendy Craig
- Biosafety Group International Centre for Genetic Engineering & Biotechnology (ICGEB) Italy
| | | | | | | | - Jörg Romeis
- Research Division Agroecology and Environment Agroscope Switzerland
| | - Richard Shaw
- Centre for Agriculture and Biosciences International (CABI) United Kingdom
| | - Claus Svendsen
- Ecotoxicology and Chemical Risk Group United Kingdom Research and Innovation Centre for Ecology and Hydrology (CEH) United Kingdom
| | | |
Collapse
|