Genomics is routinely used across many livestock and plant breeding industries. It is now practical, within certain considerations, to consider applying genomic selection to aquaculture breeding programs due to significant cost reductions in the last decade. Its use in aquaculture breeding programs is increasing and genomics has already been researched for oyster breeding by USC (Vu et al. 2021a; Vu et al. 2021b).

Genomic selection has the potential to reduce the cost of estimating breeding values, which presently is a costly and challenging exercise with SROs and also may potentially increase genetic progress and selection accuracy for the SRO BP. The research proposed in this application will evaluate if it is possible to increase genetic progress for the productivity traits of QX disease resistance and growth as well as the product quality trait of meat condition. Increased QX survival and growth are particularly important traits for the SRO industry at this current time due to Port Stephens, the second largest SRO producing estuary in NSW, reeling from the impact of QX disease outbreaks. Climate change resilience is a new trait being investigated for incorporation into the breeding program for industry to respond to this threat. We would also like to assess whether genomics can provide a pathway to increase selection for resilience.

This project has been developed in line with the Oysters Australia Strategic Plan 2020 and the FRDC R&D Plan 2020-2025. The outcomes from this project will assess the feasibility of increasing selection accuracy for traits that improve productivity (growth and meat condition) as well as reduce impacts caused by QX disease and climate change through breeding for resilience. The outcomes will assess the possibility to improve genetic selections for multiple traits such that oysters can be selected on their ability to adapt to new climate conditions, survive QX disease whilst having faster growth and better meat condition. Additionally, this project will build new knowledge skills and networks through a NSW DPI, The University of the Sunshine Coast and The University of New South Wales alliance as well as create post-doctoral study opportunities. These meet the goals in Program 1, 2 and 3 outlined in the 2020-2025 Oysters Australia Strategic Plan.

With respect to the FRDC R&D Plan 2020-2025, this project will build capacity and create knowledge through developing skills and networks between NSW DPI, The University of the Sunshine Coast and The University of NSW to breed oysters that offer oyster businesses greater profitability, reduced risk and that can adapt to changing environments.

This project will explore alternative methods to what is presently used for SRO breeding to assess feasibility of genomic selection and what might be required today to move towards genomic selection in the future. This project will start compiling a reference library for SROs that can be used in the future and promote innovation in SRO breeding to integrate the technology developed from this project. Moreover, costs associated with genomic selection are reducing which increases the value proposition for incorporation into the future. The ultimate success and transfer of outcomes from this project to end user beneficiaries will be through incorporation of these new technologies into the SRO breeding program.

The lack of knowledge on fundamental fisheries biology, uncertainty in stock structure, population dynamics, and cross-sectoral harvest levels, means that current stock assessments are unequipped to reliably determine stock status or inform recommended biological catches (RBCs), and that management of the resource occurs within a high degree of uncertainty. These EXCEPTIONAL INCREASES IN HARVEST and UNCERTAINTY SURROUNDING SUITABLE RBCs create an URGENT NEED TO DEAL WITH THE SUBSTANTIAL KNOWLEDGE VACUUM FOR THIS RESOURCE. Without this improved knowledge, the reasonable assessment of the status of the resource, estimation of appropriate harvest levels, harvest strategy development, implementation of appropriate management, and informed decision making on how best to utilise the resource, will continue not to be possible. Furthermore, environmental variability and species-habitat-fishery interactions are likely to impact stock dynamics and biomass, which in turn affects the magnitude, profitability, and social outcomes derived from the resource. Thus, efficient exploitation and effective management of the resource within a harvest strategy framework cannot occur without: 1) spatial definition of likely management units (stock structure); 2) estimates of stock biomass within those units; 3) estimates of basal population parameters and some appreciation of the influence of environmental stochasticity on resource productivity; and, 4) an appreciation of resource access across sectors. There is likely potential for further development in this fishery, to satisfy growing markets for the species both locally and abroad, but this will never be realised until these information needs are met.