Development of optimal molecular markers of domestication in Atlantic salmon for assessing introgression in wild populations

Lead Research Organisation: University of the Highlands and Islands
Department Name: Inverness College UHI

Abstract

Controversy surrounds the actual impacts of Atlantic salmon farming on wild salmonid stocks, fed by the lack of direct evidence for or against many potential impacts, with uncertainty an increasing impediment to sustainable industry development and effective management of wild stocks. This applies to the potential impact of the introgression of farm genomes into locally adapted wild populations from breeding of farm escapes. Escapes do occur and are recognized as inevitable, but are a very small fraction of farm stocks and vary in numbers both locally and temporally. The majority of escapees are expected to die without breeding but some do remain in or ascend rivers and spawn. However, a detailed understanding of actual levels of interbreeding and introgression in most rivers is lacking which, along with an understanding of the adaptive differentiation of farm and wild salmon, is required to establish the actual impact of this potential interaction on the productivity and viability of wild populations.

Detection and quantification of interbreeding and introgression requires diagnostic markers for farm and wild genomes. Genetic differentiation of farm and wild genomes can evolve through founder effects, selective breeding and domestication selection and is observed in respect of a variety of molecular markers. However, existing molecular markers are not fully diagnostic and regionally constrained in their usefulness. Unfortunately, marker panels screened for useful variation have been small and arbitrary such that they are unlikely to include the most informative loci and to be context specific, limiting their power and transferability. To properly address the issue of introgression molecular markers are required that are highly diagnostic across all farm and wild populations. These markers will be in genomic regions involved in domestication and controlling the expression of selected economic traits.

What is known of the genomic architecture of domestication and most economic traits indicates their control is polygenic, making the targeting of specific gene regions in the search for markers difficult. In contrast, recent advances in genomics make possible genome scanning and genome-wide association studies (GWAS) which can provide a high resolution assessment of molecular differentiation between different individuals or populations across the genome. Different GWAS strategies can be employed but two are deemed optimal in the current context. Firstly, a GWAS will be carried out using a new Atlantic salmon SNP (single nucleotide polymorphism) containing 930k nuclear SNPs, recently developed in collaboration with the salmon farming industry. This will be carried out on a broad base of representative farm and wild stocks. Secondly, GWAS will be carried out to identify temporally stable epigenetic DNA-methylation base changes induced by rearing fish in culture by comparing groups of single source wild fish reared in the wild and in culture.

The study will deliver the first general understanding of domestication related molecular genetic differentiation between farmed and wild salmon and identify the best markers for identifying farm salmon in the wild and assessing genetic introgression of farm genes into wild populations. The work will deliver a more robust and generally applicable tool for determining the actual levels of escapes and introgression in wild salmon populations. Following field calibration and independent validation, the diagnostic methodology defined in the study is expected to provide the basis for generating the evidence needed to clarify the debate on levels of escapes and introgression and the long term impacts of introgression on population viability. This will help to define more clearly the path forward for the sustainable development of the salmon farming industry in the UK and elsewhere in the North Atlantic region and help to inform management priorities for wild Atlantic salmon stocks.

Technical Summary

The proposed research programme will survey direct DNA base variation and epigenetic DNA base methylation changes in farmed Atlantic salmon strains and wild stocks to identify diagnostic heritable differences. Replicated pooled samples (50 individuals in each pool) will be used to screen 12 different farm strains and 12 different wild stocks from Scotland, Ireland, Norway and Canada, spanning the range of Atlantic salmon, will be screened on a 930,000 Affymetrix SNP array. Estimates of allele frequencies for each SNP will be made for pools based on normalised theta values of the cluster positions of the different genotypes and differences will be assessed across all farmed-wild comparisons as well as similarity in the directionality of differences among farmed strains. Coupled with tests for 'outlier' loci, this will be used to identify the top-ranked SNPs for discrimination. The genomic positions of these SNPs will be mapped using existing linkage information to identify regions associated with domestication. The top 300 ranked SNPs will be further screened for individual genotypes on 300 fish from across the study to validate allele frequency estimates derived from pooled samples. Epigenetic analysis will focus on identifying stable DNA methylation changes induced by rearing fish in culture. Eggs from different wild-origin families will be divided across two experimental groups reared under captive or semi-natural conditions. Male parr from the two groups will be screened for maturation stage and sperm collected for both methylation analyses and egg fertilisation according to a fully factorial breeding design. Embryos from each family will be sampled at an identical developmental stage and analysed for methylation status. Reduced Representation Bisulfate Sequencing on an Illumina HiSeq will be used, to analyse both the sperm of the two experimental groups as well as in embryos fertilised by the two types of sperm (wild and cultured).

Planned Impact

The findings will have impact on our understanding of our capacity to monitor and manage direct genetic interactions, and will establish a major step change towards the development of the molecular markers and analytical tools available to managers and regulators. It will be of great value to the regulatory and non-academic community in providing a more robuts appreciation of the nature and extent of the genetic differentiation underlying the adaptive differences between wild and domesticated stocks of Atlantic salmon. The stakeholder community in the UK that will make use of this information to inform the management of wild stocks will be the North Atlantic Salmon Conservation Organisation (NASCO), the Atlantic Salmon Trust (AST), the Rivers and Fisheries Trusts Scotland (RAFTS), the Rivers Trust (England); it is these organisation whom will be targeted for delivery of a non-technical overview of project findings and with whom opportunities will be explored to make public presentations of the science carried out and its findings. Each of these organisations is concerned with the welfare and health of wild salmon populations and engages with scientific bodies, academic communities and the aquaculture industry. Furthermore, government agencies such as Marine Scotland, the Department of Fisheries and Oceans (Canada) and other regulatory bodies in other salmon or aquaculture countries will be end-users of the new understanding and the identified tools to assist them in taking management decisions involving the conservation of wild stocks as well as the regulation of aquaculture industry development. Partners in the proposed project cover the scientific branches of government agencies (in addition to academic partners), thereby creating direct links to their relevant regulatory bodies. By furthering our understanding of the occurrence and degree of genetic interactions between farmed and wild salmon stocks, this work will help to progress the dialogue between wild fish interests and those of the aquaculture industry. It is only by understanding the degree to which genetic interactions among farmed and wild salmon may pose a risk that measures can be taken to ensure both the continued conservation of wild stocks, while allowing for increased expansion of the industry, both of which offer great economic resources to many regions. At the same time, the project results can be exploited by the aquaculture industry with regards to using the information to improve the performance in culture of farmed stocks by helping to define the regions where genes have been selected for to improve overall performance. Thus the findings of the project will also be of interest and communicated to the salmon farming industry through their trade organisation the SSPO whom will be included in the Stakeholder Workshop that will be held at the end of the project.
 
Description We have been able to provide evidence of 1) the regions of the Atlantic salmon genome that are involved in the domestication of the species, 2) DNA variants that can be used to universally discriminate domesticated, farm fish from wild fish as well as fish that are of first generation mixed farm-wild ancestry, and assess at a population level overall levels of introgression of farm genes into wild populations, 3) epigenetic changes that arise from the rearing of fish in controlled culture conditions.
The SNP marker set developed shows that the genetic architecture of Atlantic salmon domestication to be complex with domestication related genes distributed throughout the genome though variation in 3 gene regions on 3 chromosomes appear to be particularly important. Despite this a set of SNP markers that collectively give a high level (>95%) of success in discriminating farm fish, much higher than existing panels, was able to be identified for use in Scotland and likely to be useful in other regions as well such as Iceland and Norway.
Exploitation Route The findings will be published in peer-reviewed journals. The DNA variation marking domestication will be applied to assessing and monitoring levels of farm escapes and introgression in wild populations to inform management and policy in relation to salmon farming in Scotland as well as elsewhere in the species range. Information on genomic regions associated with domestication as well as understanding gained of epigenetic change will be used to design further research and funding applications to generate a more specific understanding of the specific genes involved in domestication as well as those involved in epigenetic change.
Sectors Agriculture, Food and Drink,Environment,Government, Democracy and Justice

 
Description The findings have been used in the development of an optimal panel of SNP markers for the identification of farm salmon and the assessment of levels of introgression of genes from feral farm salmon into wild populations. The SNPs identified by the project have proven to be superior in their ability to achieve these objectives than existing marker sets and the new panel is dominated by markers developed by the project.
Sector Agriculture, Food and Drink,Environment,Government, Democracy and Justice
Impact Types Societal

 
Description ICES Workshop
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Impact This has led influenced policy development in the North Atlantic Salmon Conservation Organization and through it national policy on salmon management across the North Atlantic.
URL http://www.nasco.int/pdf/reports_other/2016ThemeBasedSession.pdf
 
Description Icelandic Farm Management Regulations
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact The policy on which advice was given has now been implemented by the Icelandic government and provides an enlightened adapative management approach to ensuring the sustainable development of salmon farming in Iceland
URL https://www.hafogvatn.is/
 
Description Parliamentary Committee
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
URL http://www.gov.scot/Publications/2002/08/15170/9406
 
Description Screening of wild salmon for introgression of farm genes
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Made it feasilble to put in place an accurate system of monitoring wild salmon populations for the presence of feral farm escapes and the introgression of farm genes into wild salmon populations. The main impacts of the research output will start in 2019 when the program of screening of wild populations by the Scottish government will begin.
 
Description European Social Fund (ESF) PhD Studentship
Amount £123,000 (GBP)
Organisation Government of Scotland 
Department Scottish Funding Council
Sector Public
Country United Kingdom
Start 10/2018 
End 03/2022
 
Description European Social Fund (ESF) PhD Studentship
Amount £123,000 (GBP)
Organisation Government of Scotland 
Department Scottish Funding Council
Sector Public
Country United Kingdom
Start 04/2018 
End 10/2021
 
Title Universal Marker set for assessing farm wild interbreeding 
Description A universal set of markers for testing whether salmon are of farm, wild or hybrid farm wild origin 
Type Of Material Biological samples 
Year Produced 2018 
Provided To Others? No  
Impact This tool will be published in the public domain in 2018 
 
Description Informing modelling of genetic interactions of feral farm and wild salmon populations 
Organisation Department of Fisheries and Oceans Canada
Country Canada 
Sector Public 
PI Contribution The project started as an informal collaboration established and led by the PI involving a number of partners in academia, industry and government agencies, and researchers from UK, Norway, Ireland and Canada. This network subsequently lead to the PI and Researcher Co-I participating in a large consortium led by Fisheries and Oceans Canada and encompassing three international knowledge transfer workshops on focused on methods and gathering of data needed for modelling the demographic and genetic interactions between farm and wild Atlantic salmon and on the advancement of analytical predictive modelling methods and programmes. Workshop 1: Galway, Ireland - 7-9 March 2017; Workshop 2: Inverness, Scotland - 3-5 October, 2017; Workshop 3: Reykjavik, Iceland - 13-15 Nov, 2018. The PI and Co-I have contributed to discussions and presentations at all three workshops, encompassing primarily the findings of the BBSRC project.
Collaborator Contribution The partners contributed to the BBSRC project by the provision of samples and sponsoring of the international workshops on modelling where a number of the international partners for the project attended. Samples helped with the development of informative marker sets and workshops with defining the data input to meet the requirements for modelling e.g. levels of farm escapes, levels of introgression, that can be informed using molecular marker based tool being developed. The participants also provided input into the optimal approaches to the data analysis and discussed the development of future collaborations.
Impact Not as yet but a number of potential peer-reviewed publications are being developed.
Start Year 2015
 
Description Screening of juvenil salmon for evidence of escapes and gene introgression from farm smolt rearing in freshwater lochs 
Organisation Lochaber and District Fisheries Trust
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution The research programme design was led by us and all the genetic screening and data analysis will be carried out by us. We will deliver an internal report of our results.
Collaborator Contribution Mowi and the two Fisheries Trusts helped with the design of the field sampling programme. Mowi will provide smolts from the loch cages and the Trusts will undertake the electofishing of wild populations and both will provide tissue samples to us.
Impact None as yet. Multi-disciplinary in so far as involves genetics and field biology working with fisheries management.
Start Year 2019
 
Description Screening of juvenil salmon for evidence of escapes and gene introgression from farm smolt rearing in freshwater lochs 
Organisation Mowi Scotland
Country United Kingdom 
Sector Private 
PI Contribution The research programme design was led by us and all the genetic screening and data analysis will be carried out by us. We will deliver an internal report of our results.
Collaborator Contribution Mowi and the two Fisheries Trusts helped with the design of the field sampling programme. Mowi will provide smolts from the loch cages and the Trusts will undertake the electofishing of wild populations and both will provide tissue samples to us.
Impact None as yet. Multi-disciplinary in so far as involves genetics and field biology working with fisheries management.
Start Year 2019
 
Description Screening of juvenil salmon for evidence of escapes and gene introgression from farm smolt rearing in freshwater lochs 
Organisation Ness & Beauly Fisheries Trust
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution The research programme design was led by us and all the genetic screening and data analysis will be carried out by us. We will deliver an internal report of our results.
Collaborator Contribution Mowi and the two Fisheries Trusts helped with the design of the field sampling programme. Mowi will provide smolts from the loch cages and the Trusts will undertake the electofishing of wild populations and both will provide tissue samples to us.
Impact None as yet. Multi-disciplinary in so far as involves genetics and field biology working with fisheries management.
Start Year 2019
 
Description ARCH-UK Annual Science Event 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact The activity was a workshop focused on early career researchers in the aquaculture sector as well as an update on past, present and fture research activity in the sector. The purpose was to help ECRs to develop their careers in the sector and for workers in the sector to exchange knowledge and move research in the sector forward.
Year(s) Of Engagement Activity 2018
 
Description Aquaculture Europe Conference - Croatia 
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 A presentation was made entitled:
Deiene Rodriguez Barreto, Tamsyn Uren-Webster, Mark Coulson, Eric Verspoor, Carlos Garcia de Leaniz, Sofia Consuegra
Epigenetic markers of domestication for assessing farm introgression in salmon wild populations
Year(s) Of Engagement Activity 2018
 
Description Aquacutlure Open Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Invasive Species Day at Oriel Science
Public · Hosted by Oriel Science
Year(s) Of Engagement Activity 2017
 
Description Farm wild salmon Interactions modelling workshop 
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 It was a professional workshop to advance the use of modelling to understand and predict the impact of escaped farm salmon on the genetics and viability of wild salmon populations.
Year(s) Of Engagement Activity 2018
 
Description Genomics in Aquaculture (GIA 2016) 
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 A presentation was made entitled:
Epigenetic management of stress and disease resistance in farmed and inbred fish
Sofia Consuegra
Year(s) Of Engagement Activity 2016
 
Description ICES Working Group on the Application of Genetics to Fisheries and Aquaculture 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact The working group considered the implications of recent advances in understanding of indirect genetic impacts of farm salmon on wild populations of fish generally and how to advance understanding and inform policy and the management of such impacts.
Year(s) Of Engagement Activity 2018
 
Description ICES Workshop 
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 The PI and Researcher Co-I participated in an ICES Workshop to formulate and deliver in report form to NASCO (North Atlantic Salmon Conservation Organisation) advice on the possible effects of salmonid aquaculture on wild Atlantic salmon populations in the North Atlantic
Year(s) Of Engagement Activity 2016
 
Description II JOINT CONGRESS ON EVOLUTIONARY BIOLOGY 
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 A paper was presented entitled:
Sofia Consuegra, Deiene Rodriguez Barreto, Tamsyn Uren-Webster, Mark Coulson, Eric Verspoor, Carlos Garcia de Leaniz
Epigenetic signatures of fish domestication and the potential for epigenetic introgression between captive and wild populations
Year(s) Of Engagement Activity 2018
 
Description International Modelling Workshop 
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 None known as yet beyond dissemination of research to date and input of expert opinion to further data analysis and marker development
Year(s) Of Engagement Activity 2017
 
Description NERC Unearthed 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact eDNA - Public engagement -Interactive exhibition offering people of all ages the chance to get closer to DNA, eDNA and environmental sciences.
Year(s) Of Engagement Activity 2017
 
Description Techniquest Welsh Science and Discovery Centre 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Public Engagement. Development of an Interactive exhibition to a broad audience/ school programmes to be set at Techniquest.
Year(s) Of Engagement Activity 2017
 
Description University Federal do Rio Grande do Norte 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact A talk was given:
Epigenetic signatures in domesticated and wild fish species
Sofia Consuegra & Carlos Garcia de Leaniz
Year(s) Of Engagement Activity 2019
 
Description Wales Gene Park Roadshow 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact A presentation was made:

The Role of Epigenetic Inheritance in Conservation Genetics
Sofia Consuegra
Year(s) Of Engagement Activity 2018