Application of genetic markers to improve resistance to herpes virus in commercial oyster populations

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

Background:
Pacific oyster (C. gigas) is one of the most important aquaculture species in the world, but sustainable production is threatened by outbreaks of Oyster herpes virus (OsHV), which can cause high mortality rates. There is substantial host genetic variation in resistance within farmed stocks. Therefore, improvement of survival rates via selective breeding has the potential to form a major component of disease control. However, UK oyster production does not yet have the capacity to produce more resistant stocks, because structured selective breeding schemes for shellfish do not exist. As part of an ongoing BBSRC-NERC sustainable aquaculture award, the Roslin Institute, Cefas and Edinburgh Genomics have developed the first high density single nucleotide polymorphism (SNP) array for oysters. In parallel, a laboratory virus challenge experiment has been successfully performed. The resistant and susceptible oysters from this trial are being genotyped to map resistance loci in the oyster genome. The major practical outcome will be SNP markers that can predict which oysters are resistant to the disease.

Project Partners and Challenges:
The lack of selective breeding for shellfish in the UK presents significant challenges (and opportunities) for UK production; namely (1 - short term) to identify and breed from parent oysters with high resistance to OsHV-1, and (2 - long term) to move towards well-managed selective breeding of oysters to harness genetic variation to improve key traits. The Roslin institute will work with Cefas and UK oyster hatcheries Guersey Sea Farms Ltd and Seasalter Shellfish Ltd to address these challenges. They will also work with the Cawthron Institute (New Zealand), who are world leaders in shellfish breeding and reproduction, but do not yet apply modern genomic tools in their breeding programmes. The project directly contributes to the themes of the call relating to "Breeding and genetics approaches for stock enhancement" and "Monitoring and control of health and disease".

Aims and Objectives:
The primary aim of this project is to apply genetic markers to breed oysters with improved resistance to oyster herpes virus in the farm environment. The specific objectives of the proposed project are:
(i) To verify SNP markers associated with OsHV resistance using samples and data from commercial oyster populations during field outbreaks.
(ii) To establish a process within a commercial hatchery for marker-assisted selection for resistance using parental oysters.
(iii) To test genomic prediction of breeding values for OsHV resistance in an oyster population with pedigree and trait records.
(iv) To determine the most (cost) effective method of using genetic markers in oyster breeding to improve disease resistance.

Project Outputs and Impacts:
The project team will work closely with commercial partners to deliver tangible outputs that will help address the aforementioned challenges. Testing of SNP markers of resistance in field outbreaks in independent populations to the discovery population will enable a genetic test for OsHV resistance to be created. This will be applied to the oyster aquaculture industry by working with commercial hatchery partners, and developing a system to genotype parent oysters for marker-assisted selection. Concurrently, the utility of genomic prediction (use of genome-wide markers to predict breeding values) will be assessed at different marker densities. This will result in a report on the most (cost) effective means of using genetic markers to breed for disease resistance in oysters.

Project Duration and Cost:
The project will last 24 months and will have a total cost of £199,741.

Planned Impact

This project will involve academic, government and industry partners, who will work to apply genomic tools and knowledge developed previously by our team in a commercial setting. The major output of this project will be (improved) methods of selecting oysters with high resistance to Oyster Herpes Virus for commercial aquaculture. This will be achieved via the following specific outputs

1. Field validation of candidate SNP markers found to be associated with resistance to OsHV in the laboratory setting (with Guernsey Sea Farms and Sea Salter)
2. Implementation of marker-based tests of resistance to OsHV-1 in a UK commercial hatchery (with Guernsey Sea Farms and Sea Salter)
3. Genomic prediction of breeding values for resistance to herpes virus in an advanced selective breeding programme (with Cawthron).
4. Defining the most (cost) effective route of applying genetic markers to breed for disease resistance in oysters (all partners)

There are clear short and long term impacts of the proposed project for the partners, and for sustainable shellfish production in the UK and internationally. These include:

1. Improved innate resistance of UK farmed oyster populations to OsHV, leading to reduced incidence and severity of disease outbreaks.
2. Establishing an exemplar process for implementation of modern breeding techniques into UK oyster hatchery production. If successful, the longer term impact could be a drive to implement selective breeding for improved oyster stocks in the UK industry.
3. Implementation of the SNP array in the Cawthron samples will enable improved accuracy of selection in their programme, and ensure global impact of UK-developed knowledge and technology.
4. Successful use of this technology in NZ oysters will potentially increase interest in genetic analysis in many other selectively bred commercially important aquaculture species, in a country with a hugely proactive aquaculture industry. The longer term impact could be transfer of skills and knowledge from the NZ industry to improve UK shellfish production.

Publications

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Houston R (2017) Future directions in breeding for disease resistance in aquaculture species in Revista Brasileira de Zootecnia

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Palaiokostas C (2017) Genome-wide approaches to understanding and improving complex traits in aquaculture species. in CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources

 
Description There are two major outputs of the project to date that are new / innovative. The first is the first successful example of genomic selection in oysters. This has generated significant interest amongst the academic and commercial community. The first paper showing this is linked here. https://www.frontiersin.org/articles/10.3389/fgene.2018.00391/full
A key result here was that low marker density genomic selection can be a cost-effective method for oyster breeders to use to improve their strains. These results were very interesting for The Cawthron Institute in New Zealand who run advanced breeding programmes for shellfish. They were also presented to the EU Vivaldi project http://www.vivaldi-project.eu/ as an example of use of molecular genetics to improve breeding, at the Aquaculture Europe conference in 2018.
Exploitation Route The impact already achieved has been via disemination of results related to genomic selection in oyster, which has informed the academic and commercial oyster breeding communities on optimal methods for using genetic markers to improve resistance to virus. This will be a long term impact. The shorter term impact has been the implementation of the process of marker-assisted selection in UK oyster hatcheries, in particular by Guernsey Sea Farms. This will help UK oyster production move towards genetic selection and improvement of disease resistance as a novel way to prevent infectious diseases.
Sectors Agriculture, Food and Drink

 
Description The research has led to validation of genetic markers associated with resistance to herpes virus in oysters, which causes high levels of economic losses in oyster aquaculture. The outputs have been taken up by oyster hatcheries in the UK, including Guernsey Sea Farms and SeaSalter, who are working with use to develop methods of screening oysters for testing of genetic markers prior to breeding. Further, we are working with Blue Marine Foundation to trial similar technology for application to restocking native oysters with high innate resistance to parasitic disease. Finally, we are working with the Cawthron Institute and have genotyped their oyster lines, which will allow Cawthron to apply genomic selection for resistance to disease in their advanced breeding programmes.
First Year Of Impact 2017
Sector Agriculture, Food and Drink
Impact Types Societal,Economic,Policy & public services

 
Description Advancing European Aquaculture by Genome Functional Annotation
Amount € 6,000,000 (EUR)
Funding ID 817923 
Organisation European Union 
Sector Public
Country European Union (EU)
Start 05/2019 
End 04/2022
 
Description Research Grant - Ross Houston - Investigating genetic resistance to Bonamia in European flat oyster
Amount £165,026 (GBP)
Organisation Blue Marine Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 07/2018 
End 06/2020
 
Description Standard Grant - Ross Houston - AquaLeap: Innovation in Genetics and Breeding to Advance UK Aquaculture Production
Amount £403,285 (GBP)
Funding ID BB/S004343/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2019 
End 12/2021
 
Description Collaboration with Cawthron Institute in New Zealand 
Organisation Cawthron Institute
Country New Zealand 
Sector Charity/Non Profit 
PI Contribution This collaboration is built around a BBSRC partnering award in which I was the UK PI (BB/N022114/1 New Zealand - UK Paterning Award: Breeding for disease resistance in farmed oysters using genomic tools). The idea is to merge the genomic tools and skills that we have developed in the UK with the advanced shellfish selective breeding programmes that Cawthron run in New Zealand. Our research team has, for example, developed a high density SNP genotyping array for farmed oysters - the first of its kind for this species.
Collaborator Contribution Cawthron have world-leading selective breeding programmes for shellfish, including Pacific Oysters. One of the main target traits is to increase resistance to Oyster Herpes Virus (OHV) which can decimate stocks on oyster farms. They are providing our collaborative projects with access to extensive samples and data from their pedigreed oysters which have been challenged with OHV, in addition to their time to manage and run the project and provide intellectual input.
Impact Funded collaborative grant: NE/P010695/1 Application of genetic markers to improve resistance to herpes virus in commercial oyster populations This grant application builds on the BBSRC travel award and will provide funds for genotyping Cawthron's pedigreed oyster material with our high density SNP array developed under the BBSRC Aquaculture Initiative project BB/M026140/1 Investigation of Host Genetic Resistance to Oyster Herpes Virus using a High Density SNP Array. The downstream impact will be improved selective breeding for disease resistance in oysters, and transfer of much needed skills and expertise in advanced shellfish breeding from NZ to the UK. These collaborations also involve the Centre for Environment, Fisheries and Aquaculture Science (Cefas). The collaboration brings together expertise in genomics, sequencing, selective breeding, shellfish biology and virology.
Start Year 2016