ROBUST-SMOLT Impact of early life history in freshwater Recirculation Aquaculture Systems on A. salmon robustness and susceptibility to disease at sea
Lead Research Organisation:
University of Edinburgh
Abstract
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Technical Summary
The adoption of Recirculation Aquaculture Systems for freshwater salmon production has clear benefits however, fish transferred from RAS systems are not performing equally to fish reared in open water loch systems. In the current project, we hypothesise that RAS rearing conditions, especially water chemistry and microbiology, nutrition, photoperiod and temperature, affect early life history traits of salmon and impact on microbiomes, immune barriers, osmoregulation, and robustness at sea especially for gill pathologies and new anaemic syndrome. The proposed research is multidisciplinary and will develop basic knowledge on RAS, photo-thermal history, diet and vaccine effects on fish physiology that may predispose fish to disease at sea. Two large-scale trials will be performed to test RAS vs. open water lochs in a commercial setting and the interaction between photoperiod, diet and vaccine in a controlled experiment. In addition, small-scale experiments will test the effects of increased CO2 on salmon physiology, the effects of freshwater history on smolt immune function (using double stranded RNA challenge) and post-smolt amoebic gill disease susceptibility when challenged with infectious agent N. Peruvans. A toolbox will be used to study fish health biomarkers including blood chemistry, haematopoietic indexes, endocrine status and immune function including leukocyte inflammatory markers, anti-viral response in erythrocytes and plasma prostaglandins. The genotype by environment interaction will also be studied. Experimental and production data will be combined in a meta-analysis to produce a unique large-scale epidemiological study and identify risk factors for disease at sea. Major outcomes will be industry recommendations, protocols and tools for early freshwater conditioning that promote enhanced immune function and health at sea. The ROBUST-SMOLT project will contribute to boost the competitiveness and sustainability of the UK aquaculture sector.
Planned Impact
See Lead Institution Form
Publications
Mucha S
(2022)
Animal Board Invited Review: Meta-analysis of genetic parameters for resilience and efficiency traits in goats and sheep.
in Animal : an international journal of animal bioscience
Doeschl-Wilson A
(2021)
Review: Livestock disease resilience: from individual to herd level.
in Animal : an international journal of animal bioscience
Chase-Topping M
(2021)
Impact of vaccination and selective breeding on the transmission of Infectious salmon anemia virus
in Aquaculture
Douhard F
(2022)
The cost of host genetic resistance on body condition: Evidence from divergently selected sheep.
in Evolutionary applications
Saura M
(2019)
Disentangling Genetic Variation for Resistance and Endurance to Scuticociliatosis in Turbot Using Pedigree and Genomic Information.
in Frontiers in genetics
Knap P
(2020)
Why breed disease-resilient livestock, and how?
in Genetics Selection Evolution
Pooley C
(2022)
Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission.
in Genetics, selection, evolution : GSE
Tsairidou S
(2019)
Enhancing genetic disease control by selecting for lower host infectivity and susceptibility.
in Heredity
Makau D
(2022)
Ecological and evolutionary dynamics of multi-strain RNA viruses
in Nature Ecology & Evolution
Bailey R
(2020)
Pathogen transmission from vaccinated hosts can cause dose-dependent reduction in virulence
in PLOS Biology
Pooley CM
(2020)
Estimating individuals' genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data.
in PLoS computational biology
Petersen GEL
(2022)
Modeling suggests gene editing combined with vaccination could eliminate a persistent disease in livestock.
in Proceedings of the National Academy of Sciences of the United States of America
Robinson N
(2022)
Applying genetic technologies to combat infectious diseases in aquaculture
in Reviews in Aquaculture
Anacleto O
(2019)
Genetic differences in host infectivity affect disease spread and survival in epidemics.
in Scientific reports
Gratacap RL
(2019)
Potential of Genome Editing to Improve Aquaculture Breeding and Production.
in Trends in genetics : TIG
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
| Description | Genotype by environment (RAS vs Loch) interaction (GxE) of Atlantic Salmon was assessed by measuring the impact of freshwater environment on performance traits in sea water. The population originated from Atlantic Salmon commercial stock located at MOWI Ireland. Broodstock had been selected for growth (body weight), greater resistance to cardio myopthaty syndrome (lower heart damage score) and lower proportion of early sexual maturity. A total of 140 families were produced from hierarchical mating strategy. In January 2021, approximately 250,000 eyed eggs were transferred to recirculating aquaculture facilities (RAS) in the northwest of Scotland. After sex identification, a total of 91,708 fish (32,584 females and 59,124 males) were moved to freshwater loch environment where each sex was held in a separate net pen. In addition, 91,713 fish were kept in the RAS, 45,874 females and 45,839 males, each gender in a separate tank. Later, fish from the loch and RAS environments were transferred to saltwater net pens in the northwest of Scotland. The population was sampled at the end of the freshwater rearing, prior to saltwater transfer. A total of 1,000 fish were sampled per environment, split between 250 males and 750 females. Fin clips were taken from adipose fin for genotyping by using 50K SNP of IdentiGEN Ltd. Measurement of whole-body weight (WBW) (g) and length (cm, tip of head (snout) to deepest point of the fork in the caudal fin) were taken and from which a condition factor (W/L3) (K) was calculated. For each trait, variance components and heritability were estimated using univariate animal model via implementation of a restricted maximum likelihood (REML) approach using BLUPF90 software. To estimate the effect of GxE, a multi-trait approach was used where the same trait measured in different environments was treated as two independent traits. Results indicate that the RAS environment produced significantly smaller smolts, but with greater uniformity and heritabilities across all traits compared to the loch environment. The Loch environment produced a greater variation in all studied traits, contained both the largest and the smallest fish, leading to greater environmental/residual variance and conversely to lower heritability estimates. Between environments there was an indication of GxE in all traits, which was strongest for body weight. The health status of all fish in both freshwater and sea was generally too high to detect any impact of the early rearing environment on health in later life. Apart from the data generated within this project, no health and performance data were provided by the industrial project partners to facilitate an epidemiological study to assess to what extent the early rearing environment impacts on Atlantic salmon health at different life stages. The results indicate that future Atlantic salmon breeding programmes need to account for the impact of the early rearing environment in order to achieve the desired performance (and potentially health) at the later life stages. |
| Exploitation Route | Atlantic salmon breeders need to consider the impact of the early rearing environment in order to achieve the desired performance (and potentially health) at the later life stages. |
| Sectors | Agriculture, Food and Drink |
| Description | BBSRC Responsive Mode |
| Amount | £1,640,000 (GBP) |
| Funding ID | BB/V009818/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2021 |
| End | 08/2025 |
| Description | EU H2020 collaborative project ECO-READY- Achieving Ecological Resilient Dynamisms for the European food system through consumer-driven policies, socio-ecological challenges, biodiversity, data-driven policy, sustainable futures |
| Amount | € 14,948,450 (EUR) |
| Funding ID | 101084201 - ECO-READY |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 12/2022 |
| End | 11/2025 |
| Description | Genome editing for resistance to viral disease in rainbow trout |
| Amount | £161,786 (GBP) |
| Organisation | Hendrix Genetics |
| Sector | Private |
| Country | Netherlands |
| Start | 11/2020 |
| End | 02/2022 |
| Description | TRAnsforming the DEbate about livestock systems transformation (TRADE) |
| Amount | £677,397 (GBP) |
| Funding ID | BB/W018152/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2022 |
| End | 05/2025 |
| Description | BBSRC Singapore - Malaysia - UK Partnering Award: Genetic innovations to support sustainable tropical aquaculture |
| Organisation | Worldfish |
| Country | Malaysia |
| Sector | Charity/Non Profit |
| PI Contribution | Co-Investigator: partnership development and grant writing; provision of methods and ideas for collaborative research |
| Collaborator Contribution | all partners contributed to the partnership development and grant writing; The University of Edinburgh will host researchers from Malaysia and provide training in the UK and Malaysia |
| Impact | Approaches to incorporate genomic data into the WorldFish tilapia selective breeding programme; |
| Start Year | 2022 |
| Description | Strategic research partnership with WorldFish |
| Organisation | Worldfish |
| Country | Malaysia |
| Sector | Charity/Non Profit |
| PI Contribution | Roslin and Worldfish have a strategic research partnership since 2018 which focuses on selective breeding of Nile tilapia, one of the world's most important farmed fish species. Roslin scientists are developing genomic tools, and investigating how those genomic tools can be used to improve disease resistance of tilapia via breeding. |
| Collaborator Contribution | The partners WorldFish run a tilapia breeding programme which provides samples and data to support the research undertaken at Roslin. This breeding programme also provides the route to impact by which the improved strains can be disseminated to benefit low and middle income country fish farmers. |
| Impact | This has led to a peer reviewed publication https://www.sciencedirect.com/science/article/pii/S0044848619331837 describing genetic resistance to tilapia lake virus, which is one of the most problematic pathogens for global aquaculture. The story was presented in news form via the University of Edinburgh https://www.ed.ac.uk/edinburgh-infectious-diseases/news/news/genetic-resistance-to-lethal-virus-in-farmed-fish and also Science magazine https://www.sciencemag.org/news/2020/03/emerging-virus-killing-farmed-fish-breeders-can-help-them-fight-back |
| Start Year | 2017 |
| Description | Discussion leader at a scientific conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion group leader of the "Health and Welfare Traits" session at the Quantitative Genetics and Genomics Gordon Research Conference, Ventura, February 2023. The session informed the audience about the state of the art of genomic approaches to human and animal health and welfare, and identified research gaps, and pathways to future implementation |
| Year(s) Of Engagement Activity | 2023 |
| Description | Invited talk at an international conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at the World Congress in Genetics Applied to Livestock Production (WCGALP) 2022 on "New tools and insights to enable breeding for reduced disease transmission. " The talk informed the audience about the latest approaches to reduce disease transmission in farm animals through selective breeding |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://doi.org/10.3920/978-90-8686-940-4_168 |
| Description | Lead Organiser of the BBSRC Cross Institute workshop on "The Future Role of Livestock in Food Production |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | In this 2 day workshop, funded by the BBSRC, scientists and industry experts examined the need and scope for change in the livestock sector in response to increasing societal and environmental challenges. The outcome of the workshop resulted in a recommendation document sent to BBSRC that outlined the status quo and research and funding needs for future livestock research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ed.ac.uk/roslin/news-events/latest-news/future-of-livestock-production-in-the-spotlight |
| Description | New Scientist Future of Food Webinar |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Ross Houston took part in the New Scientist Future of Food and Agriculture workshop by taking part in a panel discussion on genome editing. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.newscientist.com/science-events/future-food-agriculture/ |
| Description | Panellist at the live online University of Edinburgh: Changing World Conversations event, Nov 2022. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | This one hour virtual event was part of the University of Edinburgh's contribution to Cop26. I was one of three panel members. Our role was to inform the public about ongoing research in agriculture to mitigate the impact of climate change and to answer questions from members from the public. Many more questions were submitted by the public that could be addressed, showing the strong interest in the field. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.youtube.com/watch?v=vFiXTAz3vbM&list=PLBcSHVMkBQZgnM7t4LFMV11oEofR2J1vX&index=4 |
| Description | Participated as one of 4 panellists in the Science Media briefing event Can We Have Our Meat and Eat It? - The Future of Meat Production" Science Media Centre London 2019 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | The briefing resulted in a wide media coverage in many regional and national newspapers, including the Guardian, The Sun, The Times etc.: Guardian https://www.theguardian.com/environment/2019/nov/28/gm-could-help-cut-livestock-methane-emissions-say-scientists PA via Hereford Times https://www.herefordtimes.com/news/national/18063917.breeding-help-cattle-become-environmentally-friendly-scientists-say/ Telegraph https://www.telegraph.co.uk/science/2019/11/27/meat-crucial-feeding-planet-going-vegan-not-green-say-scientists/ PA via iNews Clips Sky News https://news.sky.com/story/cattle-may-be-bred-to-grow-faster-and-eat-less-and-could-cut-methane-emissions-by-a-third-11871988 |
| Year(s) Of Engagement Activity | 2019 |
| Description | UKRI Climate change profile piece for Cop 26: |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | I was one of the University of Edinburgh's "climate pioneers" to contribute a short video clip describing how research on infectious disease in farm animals contributes to mitigating the impact of climate change on food security |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.ukri.org/our-work/responding-to-climate-change/our-climate-pioneers/ |