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
Department Name: The Roslin Institute

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

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Publications

10 25 50
 
Description In a commercial setting, we explored the genetic structure of growth characteristics, measure genotype-environment interactions (GxE) in salmon smolts, and examined genetic markers related to growth in freshwater lochs and RAS. Young salmon were raised together until they reached the parr stage, after which they were divided equally between freshwater net-pens and RAS.
After an eight-week period, we sampled fish from each environment and genotyped them. Our findings revealed that fish reared in RAS were generally smaller in weight and length but exhibited a higher condition factor and uniformity. We found a notably smaller component of unexplained variance in the RAS, leading to higher heritability estimates. We observed a low GxE effect for length and condition factor, but significant re-ranking for whole-body weight, as well as noticeable differences in trait associations across environments. Specifically, a segment of chromosome 22 was found to be linked with the condition factor in the RAS population only. Results suggests that if the use of RAS continues to expand, the efficiency of existing commercial populations may not reach its full potential unless breeding programs specific to RAS are implemented.
Exploitation Route The results will be of relevance to Atlantic salmon breeders and producers. They 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. As the use of RAS for Atlantic salmon production continues to expand, implementation of breeding programs specific to RAS may be required to reach high efficiency in commercial populations. Salmon producers should acquire information about the early rearing environment of their fish.
Sectors Agriculture

Food and Drink

 
Description The industry partner Mowi is taking the results of the GxE study into consideration for their new breeding programme design and research projects.
First Year Of Impact 2024
Sector Agriculture, Food and Drink
Impact Types Economic

 
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 Prevention & Control of Infectious Diseases: Epidemiology and modelling
Amount £583,602 (GBP)
Funding ID BBS/E/RL/230002D 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2023 
End 03/2028
 
Description Prevention & Control of Infectious Diseases: Understanding the basis of host resistance
Amount £502,785 (GBP)
Funding ID BBS/E/RL/230002A 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2023 
End 03/2028
 
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/