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

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.

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.