A proven requirement for sustainable and efficient primary production is well managed selective breeding programs of domesticated stock. This was recognised for Australian aquaculture in establishing the Seafood CRC Breeding for Profit Theme outcomes and strategies.

Breeding programs are long-term investments delivering incremental gains based on selection decisions made on a combination of expert advice, phenotype and genotype data analyses and sound breeding objectives. This combination, and the essential data management and analytical systems required, are beyond the scope of any single aquaculture company to provide in-house. Like the animals in the breeding program, the provision of these capabilities needs to have continuity and a long-term delivery plan.

CSIRO has over 15 years co-investment with multiple sectors of the Australian aquaculture industry in R&D to deliver commercial selective breeding programs to meet individual needs. While delivering on the R&D, CSIRO considered the strategies for its clients to obtain the required future commercial genetic services. Local options for delivering this capability are limited, partly due the current lack of programs requiring the services and the size of the programs.

As such CSIRO has developed some capability and a strategic plan (see attachment) for the transfer of the delivery of the required capabilities and systems to the predicted 8 to 10 Australian and international breeding programs to an autonomous or semi-autonomous unit by 2015 to 2017. To deliver this strategy requires additional investment in the development of the essential capabilities and systems during the transition phase from 2013 to 2015.

However critical to the strategy and further investment is the need for an independent assessment of the economic and management viability of the proposed strategy and an autonomous unit, and potential uptake by identified national and international breeding programs of the services to be provided. This critical assessment is required before further investment in establishing the proposed independent genetic services unit and in developing the essential capability and systems.

This project therefore will be in two stages with a clear Go/No-go point after the first stage. Stage 1, proposed here, will involve an independent consultant completing a Business Case assessment of the proposed strategy and services unit. Stage 2 would proceed if that Business Case proved positive and the Unit and strategy was viable and acceptable to potential clients. The second, implementation stage (which would require an updated full proposal) would involve developing the proposed Unit and training and delivering the essential capability and systems for the Unit and for the long-term viability of Australian aquaculture breeding programs.

Genetic variation
The results we have obtained in the current project are encouraging for SALTAS, as they confirm the earlier allozyme results of little loss of genetic variation. However, the results are also suggestive of a potential long term trend in loss of genetic variation. A sample collected and analysed in January 1997 (1993 year-class parents) would provide evidence to substantiate this trend or indicate whether the current results were a sampling artifact. The analysis of a 1997 sample would be the second of a proposed regular 4 to 5 year assessment of the status of the Tasmanian stock, and would help to describe the nature and speed of any long term trends.

SALTAS, as the principal Atlantic salmon hatchery in Australia, has a long term requirement to maintain industry and investor confidence in their product, and the ability to confirm the reliability of its breeding practices is important for the sustainability of the industry.

Loss of genetic variation in a cultured population will provide an early indicator of potential inbreeding, which could have grave consequences as deleterious recessive genes are exposed and stocks lose vigour dependent on genetic variance. Any loss of genetic variation in Tasmanian Atlantic salmon could be difficult or impossible to recover due to the restrictions on importation of new broodstock.

Y-chromosome marker
A number of molecular genetic techniques for trait or marker screening have been developed since the original proposal was submitted. We propose to apply some of these new techniques to the screening of Atlantic salmon DNA for a potential Y-chromosome marker. These approaches will greatly increase our chances of finding such a marker.

The new techniques we propose include:
Representational Difference Analysis (RDA);
PCR-Select cDNA Subtraction Technique;
the application of other modified subtractive hybridization and differential display techniques
that have proved useful in other species;
AFLP (amplified fragment polymorphism) technique; and
the application of a number of commercial RAPD (random amplified polymorphic DNA)
primers.

We have also established contact, and will collaborate during the proposed project extension, with workers who have a Y-chromosome marker for brook trout and arctic char, and other workers in this field working with other teleosts.

We believe that a continuation of the current project (95/80) is the best approach to further tackle this Y-chromosome marker issue. It will allow us to best utilise the expertise and momentum we have established on this problem, rather than completed our current objectives and then revisit this issue in a year or two.

If we are successful in locating a Y-chromosome marker either during the remainder of the current schedule or early in the 1997 grant extension, resources will then be directed to isolate and further characterize that marker.

Given AFMA’s need to satisfy its ESD objective, there is a need to consider uncertainty explicitly and identify performance indicators and harvest strategies that are as robust as possible to incorrect assumptions and misinformed interpretations of data. Use of these indicators and harvest strategies will improve the chances of achieving a reasonable balance between the conflicting objectives of long-term resource sustainability and the maximisation of economic gains. SEFAG's 1997 assessment plan explicitly states the need to "develop harvest strategy evaluation and performance indicators for all SEF quota species." There is a need to ensure that research and resource monitoring is conducted in a cost-effective manner (e.g. the SEF research priority to develop cost-effective fishery-independent surveys of stock abundance and recruitment indices). The results of the research will highlight the research areas most likely to improve management in the SEF.

The project also addresses two key research areas in subprogram (B) of the Wild Stock Program of the SCFA Research Committee to some extent: "Biological and socio-economic evaluation of alternative management scenarios for different species and categories of fishery to provide a framework for management planning" and "The evaluation and provision of harvest strategy models through comparison of management strategies using theory and case studies, establishing objective performance indicators for different jurisdictions and identifying options which are appropriate to the nature of the fishery".

In many states and regions around Australia there is a lack of current and reliable recreational fisheries data (e.g. participation rates, catch) that can be used in decision-making processes. Since the stock boundaries of some recreationally-important species can span several State and Federal jurisdictions, reliable stock-specific data is needed. The results of the last national recreational fishing survey undertaken in 2000-2001 are now considered outdated in many respects, or are of limited use for rarely-caught species and some fisheries or regions due to issues of scale.

Since the national survey, various recreational fishing surveys have been undertaken by State fisheries agencies to address their own specific management issues. These surveys have generally been telephone-diary approaches based on the National survey methodology. Additionally, community-based recreational fishing data collection have been undertaken at regional levels by community and recreational fishing groups. However, there has been a lack of coordination between agencies to report at a national level. Therefore, there is a need to assess the feasibility of aggregating data from these surveys to provide reliable up-to-date information at regional and national levels.