The FRDC currently has five programs:
1. Environment
2. Industry
3. Communities
4. People development
5. Extension and adoption
The Environment program (Program 1) in the FRDC’s RD&E Plan (FRDC, 2010) has four themes:
Theme 1: Biosecurity and animal health
Theme 2: Habitat and ecosystem protection
Theme 3: Climate change
Theme 4: Ecologically sustainable development
The objective of Theme 1 is to develop the capability, systems, knowledge and technologies to detect and identify pathogens to mitigate their impact on aquatic animals, ecosystems, profitability and viability.
There are 41 projects in Theme 1 divided into three clusters: (1) Salmon and Southern Bluefin Tuna
(SBT), (2) Abalone, Yellow Tail Kingfish (YTK) and Oyster, and (3) Other. The investment evaluated here is the Salmon and SBT cluster.
The group of 13 projects in the Salmon and SBT cluster focuses on health issues within Australia’s two largest aquaculture industries. The SBT aquaculture industry commenced development in 1991.
Tuna, generally about two to four years old, are captured from the wild for growing out in pontoons on aquaculture farms predominantly near Port Lincoln in South Australia. After 3 to 8 months of fattening, the fish are caught and most are exported.
Marine farming of Atlantic Salmon in Tasmania commenced in the mid 1980s. Small salmon are produced in freshwater hatcheries and are moved gradually through brackish waters to the ocean.
Growing out the salmon involves the use of cages suspended in the ocean, or in estuaries. The majority of Tasmanian salmon farms are located in the south east of Tasmania (including the Huon
River, Port Esperance and D’Entrecasteaux Channel).
Most of the projects funded in this cluster by FRDC were managed by the Aquafin CRC of which
FRDC was a contributing partner. All eight projects relating to health of Atlantic Salmon addressed amoebic gill disease (AGD). AGD is caused by amoebae that attach to the gills of the fish and impacts heavily on productivity, industry costs, and constrains industry expansion.
The five SBT projects addressed a wider range of issues including disease surveillance and detection, and the relationships between stress, management and disease.

There are 13 projects in Theme 1 (Part A) included in this analysis. Table 1 identifies the projects and
Table 2 provides a summary of each project.
Table 1: Projects Included in Theme 1 (Part A)
Project Title FRDC
Project
Number
2001/200 Aquafin CRC - SBT Aquaculture Subprogram: tuna cell line development and application to tuna aquaculture health surveillance
2001/205
2002/251
2003/225
2004/085
2004/213
2004/214
2004/215
Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: treatment and pathophysiology of Amoebic Gill Disease (AGD)
Aquafin CRC - Atlantic Salmon Aquaculture Subprogram - development of a vaccine for AGD: genomic and cDNA library screening for antigen discovery
Aquafin CRC - SBT Aquaculture Subprogram: investigation of the relationship between farming practices and southern bluefin tuna health
Aquafin CRC - SBT Aquaculture Subprogram: detection of SBT pathogens in environmental samples
Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: commercial AGD and salmon health project
Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: effects of husbandry on
AGD
Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: establishment of challenge for AGD
2004/217
2004/217.20
Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: development of an AGD vaccine: phase II
Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: development of an AGD vaccine: phase II
2004/218 Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: molecular assessment of resistance to AGD in Atlantic salmon
2006/225
2008/234
Table 2: Description of Each of the 13 projects
Project 2001/200: Aquafin CRC - SBT Aquaculture Subprogram: tuna cell line development and application to tuna aquaculture health surveillance
Project details
Aquafin CRC - SBT Aquaculture Subprogram: improving fish husbandry and performance through better understanding of the relationship of fish stress and health
ASBTIA: Investigation of causes of mortalities in farmed SBT – variation to project
2008/228
Organisation: CSIRO Livestock Industries
Period: Jan 2002 to Dec 2005
Principal Investigator: Mark Crane
Rationale The use of fish cell lines, both as a research tool and a diagnostic tool, has played a major role in the development of salmonid and cyprinid aquaculture worldwide. The commercial success of these finfish aquaculture industries is due, in part, to the development of fish cell lines which are used to monitor farmed fish populations for the presence of specific viral pathogens.

Based on the results of such health surveillance programs, disease-free stocks can be kept isolated from infected stock through restrictions in fish movements. The current lack of continuous tuna cell lines suitable for the isolation and growth of viral pathogens of tuna could be a serious obstacle to effective disease control in tuna hatcheries and nurseries which, in turn, could have a significant negative impact on the future development of the tuna aquaculture industry.
Objectives 1.
To establish primary cell cultures from southern bluefin tuna (SBT) and/or yellowfin tuna (YFT) tissues, larvae or fry.
2.
To select sub-populations of cell cultures which display continuous cell division.
3.
To clone cells which display features of immortal cell lines.
4.
To characterise the major features of the tuna cell lines important for their application as a diagnostic tool.
Outputs
5.
To determine susceptibility of cell lines to viral pathogens of marine finfish.

While the initial aim of establishing primary cultures was achieved, such cultures have restricted potential for replication, probably due to the age of
Benefits the fish used for establishing the primary cultures. Nevertheless, cultures were nurtured to encourage transformation.

Transformation was not successful and the cultures eventually died. The results demonstrated that current materials and methods are adequate for the development of primary cell cultures.

The study concluded that younger fish will be required as starting material in order to develop continuous SBT cell lines.

It is understood that a subsequent project on oxidisation of flesh tried to use the cell line, and found it was not in fact a tuna cell line but had been compromised by another line (fathead minnow).
Outcomes

Progress towards an enhanced health surveillance system through identification of disease free eggs of SBT in expectation that the life cycle of SBT can be closed and farmed fish developed from eggs rather than from wild capture where quantity limits are imposed.

Progress towards capturing potential for reducing mortality in young tuna by identifying the desirability for disease free eggs of SBT in preparation for propagating SBT rather than relying on wild capture.
Project 2001/205: Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: treatment and pathophysiology of Amoebic Gill Disease
Project details
Organisation: University of Tasmania
Period: Jan 2002 to Oct 2005
Principal Investigator: Mark Powell
Rationale There was an urgent need to develop novel treatments to reduce the impact of
AGD on the salmon industry. The growth of the industry and the ineffectiveness of freshwater bathing had resulted in the need for new treatments. The project was part of an integrated research program aligned with the development of novel treatments as well as with effective vaccine development, management and other control methods. Developing and maintaining standardised infection was crucial for vaccine testing, work in host-pathogen interaction and epidemiology. Without a quantitative

experimental model it was difficult to compare effectiveness of treatments or vaccines.
Objectives 1.
To establish an on-going laboratory source of AGD affected fish.
2.
To establish and validate a controlled infection/challenge system.
3.
To understand how AGD affects the respiratory and cardiovascular systems of Atlantic salmon.
4.
To determine how environmental parameters interact with AGD pathophysiology; in particular the interaction of temperature, oxygen, salinity, and carbon dioxide.
5.
To develop and test new chemical or pharmaceutical treatments for the control of AGD.
6.
To optimise the efficacy of current treatments by minimising the
Outputs physiological impact on the fish.

Improved understanding of the physiological effects of Neoparamoeba infection on salmon gills.

Establishment of a validated controlled infection/challenge system for use by other FRDC AGD projects.
Outcomes

Contribution to showing that any new treatments are environmentally safe
Benefits and acceptable to the public.

May assist adoption of any new treatment methods.

Potential use of the validated controlled infection/challenge system by other AGD projects.

Potential contribution to reducing costs to industry of controlling AGD and hence improved profit margins.

Potential removal of AGD as a constraint on Atlantic Salmon industry growth.
Project 2002/251: Aquafin CRC - Atlantic Salmon Aquaculture Subprogram - development of a vaccine for amoebic gill disease: genomic and cDNA library screening for antigen discovery
Project details
Organisation: CSIRO Livestock Industries
Period: Nov 2002 to Dec 2005
Principal Investigator: Chris Prideaux
Rationale There was an urgent need to develop control methods to reduce the impact of
AGD on the salmon industry. One such method that was thought worthy of investigation was that of protection via a vaccine.
Vaccine development was considered part of a multifaceted approach to develop short-, medium- and long-term solutions to the control of AGD; development of a sub-unit vaccine being the long-term approach of the overall research strategy. While a vaccine against AGD was considered a very attractive solution, it was recognised as a high risk and long-term prospect.
Objectives 1.
To characterise the genome and parasome of the AGD causative agent
Neoparamoeba pemaquidensis .
2.
To establish genomic and cDNA libraries, and screen for major parasite
DNA antigens that constitute potential vaccine candidates using DNA
Outputs sequencing together with DNA data base analysis.
3.
To use subtractive hybridisation of RNA isolated from amoeba grown in vitro and in vivo to produce a library of in vivo regulated genes.

The relative genome size of the cultured Tasmanian isolate, PA027, of

Neoparamoeba pemaquidensis was measured, and it was established that the overall research strategy was therefore logistically feasible.

Methods for the isolation of both total and polyA-RNA from crude gillisolated and cultured N. Pemaquidensis were successfully developed.

A library of up-regulated genes from infective N. Pemaquidensis using suppressive subtractive hybridisation (SSH) was created.

Bioinformatics analysis of the SSH library was carried out and led to the identification of a number of potential single candidates that may be tested as genetic vaccine antigens for AGD.

An expression/delivery vector suitable for studies of DNA vaccination of
Atlantic salmon has been constructed.

A full length cDNA library of the genes of N. Pemaquidenis has been constructed in the vector pDNR-LIB, and a library of 1,200 clones are available for immediate use in ELI based vaccine trials.

Knowledge regarding which genes may be differentially expressed between infective and non-infective N. Pemaquidensis was generated.

Availability of an efficient delivery vector and potential antigen clones for conducting experimental DNA vaccinations of Atlantic salmon for AGD was produced.
Outcomes

The outputs of this project have led to a subsequent trial of a DNA vaccine for AGD in Atlantic salmon (FRDC project 2004/217). The trial used the
Benefits modified delivery vector and N. Pemaquidensis cDNA clones generated by this project.

The cDNA library has the potential to be further utilised in biochemical and molecular studies of N. Penaquidensis and its pathogenicity.

Potential to lead to improved control of AGD through developments such as vaccines.
Project 2003/225: Aquafin CRC - SBT Aquaculture Subprogram: investigation of the relationship between farming practices and southern bluefin tuna health
Project details
Organisation: University of Tasmania
Period: Jul 2003 to Aug 2007
Principal Investigator: Barbara Nowak
Rationale While the SBT industry had a history of excellent fish health status and very low mortalities, there was a general lack of knowledge of the relationship between husbandry practices and health. There was no systematic approach to tuna health monitoring and surveillance.
Objectives 1.
To investigate the relationship between farming practices and SBT health.
2.
To develop an understanding of the epidemiology of blood fluke,
Cardicola forsteri.
3.
To develop basic best practice sampling protocols and preliminary laboratory diagnostic procedures for the SBT industry.
4.
To develop and implement a SBT health surveillance program for the tuna industry.
5.
To provide training related to SBT health.
6.
To provide SBT health research support for the biofouling project.
7.
To obtain and analyse SBT health data for a third full commercial harvest season.

Outputs

This project has promoted the understanding of SBT health, developed baseline information for farmed SBT health and methods to monitor health status of SBT.

Most husbandry procedures did not appear to affect SBT health as measured by parasite loads.

Parasites of SBT have been identified and new species described. A baseline for SBT parasite loads is now available.

The project formed a basis for monitoring SBT health.

A database for SBT health covering three farming seasons has been developed and transferred to the SBT industry. Sampling and processing protocols were developed.

The project has provided SBT health training for the SBT industry and researchers. A CD-ROM on SBT health was developed and distributed to
SBT industry and aquaculture education providers as a part of this project.

Four Honours students, one PhD student and one postdoctoral fellow were trained within the project.
Outcomes

This project has increased the understanding of the relationship between farming practices and SBT health and enhanced the industry’s ability to investigate SBT health in the future.

The methods and protocols developed for health monitoring and the industry implementation of the improved health surveillance system was a
Benefits major outcome of the investment.

Producers now have a greater capacity to anticipate and guard against fish health related incursions in tuna farms and hatcheries.
Project 2004/085: Aquafin CRC - SBT Aquaculture Subprogram: detection of SBT pathogens in environmental samples
Project details
Organisation: South Australian Research and Development Institute
Period: Jun 2004 to Oct 2007
Principal Investigator: Kathy Ophel-Keller
Rationale The current methods of parasite detection relied on the culturing of pathogens from water or sediments and were extremely laborious. There was a need for faster, specific and sensitive diagnostic tests for fish diseases. It was intended that such tests could aid in the assessment of reservoirs of disease so leading to improved control strategies.
Objectives 1.
To develop polymerase chain reaction (PCR) primers for detection of priority parasites Uronema nigricans , Cardicola forsteri and
Outputs
Neohexastoma sp.
2.
To develop quantitative assays for parasites in sediment, water and netting samples.

Calibrated quantitative DNA tests were successfully developed for three key SBT parasites, Uronema nigricans , Cardicola forsteri and Hexostoma thynni .

The tests can be used to quantify DNA of the parasites from environmental samples such as sediment, water, and sea-cage netting.

The tests are sensitive, able to detect less than 1 worm in 500g of sediment.

The detection of the DNA of C. forsteri and H. thynni in samples of

fouling organisms has helped to make significant contributions to the understanding of the biology of these parasites and the dispersal of their larvae in the farm environment.
Outcomes

The DNA tests for key pathogens can be used for both research purposes and for routine monitoring and surveillance of water, sediment or netting taken from SBT aquaculture sites.

The tests have been utilised in research including industry research studies to address research gaps regarding life cycle and distributions of the organisms.

The SARDI diagnostic laboratories now offer the assays but the demand for testing has come from researchers to date (Kathy Ophell-Keller and
Nathan Bott, pers.comm., 2012); the assays have not been incorporated
Benefits into industry surveillance programs.

Increased understanding of the life cycles of the selected parasites allowing development of improved management strategies.

Improved management strategies have been developed as result of the
DNA work; for example, the Cardicola forsteri q PCR assay was utilised to help identify the intermediate host of C.forsteri
; this has led to a new understanding of parasite biology which has aided farms to manage parasite load (Kathy Ophel–Keller and Nathan Bott, pers. comm., 2012).

Potentially quicker and more accurate detection of any build-up in parasite presence in SBT aquaculture sites, so allowing more effective remedial actions.
Project 2004/213: Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: commercial AGD and salmon health project
Project details
Organisation: University of Tasmania
Period: Jun 2004 to Sep 2007
Principal Investigator: Mark Powell
Rationale There was an urgent need to develop control methods to reduce the impact of
AGD on the salmon industry. This project continued the efforts made in earlier projects to develop short-term solutions.
Objectives 1.
To undertake commercial scale investigations into the potential use of seawater bath treatments (e.g. chloramine-T, artificially softened freshwater or hydrogen peroxide) as a strategy for AGD control.
2.
To investigate the efficacy of in feed treatments such as:
Parasiticides (e.g. bithionol)
Nutritional supplements (e.g. AquaciteTM and betabecTM)
Mucolytic agents (e.g. L cysteine ethyl ester)
Outputs
3.
To test new and novel anti-parasitic compounds for potential use in bath or in-feed treatments for AGD.

The project used a tiered screening process to identify potential candidate treatments and screen the potential efficacy of a number of disinfectant or
 potentially in-feed amoebicidal compounds.
From these studies several potentially useful in-feed amoebicides were identified, as well as compounds to promote feeding and improved
 performance in AGD affected salmon.
Some avenues of research were terminated early with industry believing no further development was necessary (for example research into the use

 of AquaciteTM and BetabecTM).
Two PhD candidates and a post-doctoral fellow were involved and trained as a part of this project.
Outcomes

There have been commercial trials by the industry for the adoption of some of the results from this project, including the use of chloramine-T as a bathing additive in seawater and the inclusion in feed of Aquacite and
Betabec.

While these treatments have been tested under commercial conditions, the results have not been sufficiently successful to warrant commercial development of these products at this stage.

The research on in-feed additives such as bithionol as an amoebicidal treatment for AGD suggest that this remains an option for further research and development for the aquaculture industry in Tasmania.

The determination of a metabolic cost for AGD provides a quantitative measure of the impact of disease management on the performance of the
Benefits
 fish, suggesting new approaches to the development of health management strategies.
Options for further research for the control of AGD were identified.
Project 2004/214: Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: effects of husbandry on AGD
Project details
Organisation: University of Tasmania
Period: Jun 2004 to Dec 2007
Principal Investigator: Barbara Nowak
Rationale There was a need expressed to expand the approach to managing AGD away from treatment approaches (freshwater bathing) only. From previous industry observations, different production strategies such as management of artificial lighting, triploids (type of stock farmed) and precocious maturation were thought to be associated with AGD impacts. Moreover, identification of husbandry approaches and understanding the reasons for reduced disease incidence within different salmon subpopulations would be valuable in other research.
Objectives 1.
To determine effects of husbandry procedures on AGD outbreaks.
Outputs
2.
To examine effects of stock (including maturation status, sex, ploidy) on
AGD outbreaks.

The project allowed on-farm assessment of effects of husbandry procedures and stock characteristics on AGD severity.

The potential to re-use fresh water for more than one bath showed promising preliminary results and further trials, including some on a larger scale should be undertaken to confirm that re-use of freshwater bath has a commercial potential.

Out of season molt subjected to artificial lighting regimes and transferred to estuarine sites, where a marked halocline is present, required earlier bathing than fish from cages where no artificial lighting was used.
However the advantage of fish subjected to artificial lighting not maturing would outweigh the disadvantage of the need for an earlier bath. This is because maturing fish were more affected by AGD than non-maturing fish.

Neither supplemental oxygenation nor high-energy diet affected AGD.


There was no statistically significant difference between males and females with regard to AGD.

There was no evidence that ploidy had an effect on AGD, however the trial

There was no significant effect of gill damage on the severity of AGD.
Outcomes

An increased understanding of the effects of husbandry on AGD.

An enhanced ability to investigate AGD in the future.
Benefits
 was compromised by the priorities of commercial farm management.
Contribution to potential to reduce impact of AGD on the salmon industry.
Project 2004/215: Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: establishment of challenge for AGD
Project details
Organisation: University of Tasmania
Period: Jun 2004 to Aug 2008
Principal Investigator: Barbara Nowak
Rationale The control of AGD by freshwater bathing imposes a very high cost on the
Atlantic salmon industry. One approach being undertaken was that of vaccine development where the supply of infective material and a means of controlled testing of candidate vaccines were considered integral to success. Consistently being able to induce AGD in fish is important to economically appraise alternative treatments and candidate vaccines before moving onto costly field trials. Inducing experimental infections is recognised as one of the cornerstones of vaccine development.
Objectives 1.
To standardise AGD challenge models (research).
2.
To use challenge models to appraise trial vaccines developed in the
Outputs vaccine development project (essential service).
3.
To provide gill-associated and cultured amoebae to collaborators (essential service).
4.
To cryopreserve virulent amoebae (research).
5.
To maintain the infection tank (essential service).
6.
To provide freshwater salmon for experiments in other projects (essential service).

Increased knowledge of AGD, in particular about the pathogen and the


 dynamics of infection.
Supply of amoebae to collaborators and a means to test novel therapeutics.
Improved understanding of risk factors.
The project described a new species of neoparamoeba, Neoparamoeba perurans , and showed that it has been consistently associated with AGD worldwide.

Stocking density, acclimation to sea water and amoeba batch variability were found to affect AGD infections.

A model to economically appraise novel treatments and experimental vaccines and other less specific means of prophylaxis such as immunomodulation.

Challenge protocols were developed, which have been successfully used and their results correlated well with field challenge.
Outcomes

Enabled progress in treatment methods and vaccine development to be
 made.
The new species discovery led to the development of new diagnostic tests, which are now available for confirmation of AGD infections and further

Benefits

 research.
The challenge protocols play an important role in assessing any new management improvements for AGD control.
Contribution to potential reduction in cost of managing AGD on salmon farms.
Project 2004/217: Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: development of an AGD vaccine: phase II
Project details
Organisation: CSIRO Livestock Industries
Period: Mar 2005 to Dec 2007
Principal Investigator: Chris Prideaux
Rationale This project continues (as phase 2) of the investment made earlier in other projects (e.g. Project 2002/251) to develop a vaccine to help manage AGD for
Atlantic Salmon aquaculture. Freshwater bathing to manage AGD was costly and was limiting farming sites due to the need for freshwater. Further, it was stressful to the fish.
Vaccine development was considered part of a multifaceted approach to develop short-, medium- and long-term solutions to the control of AGD; development of a sub-unit vaccine being the long-term approach of the overall research strategy. While a vaccine against AGD was considered a very attractive solution, it was still recognised as a high risk and long-term prospect.
This project was carried out in conjunction with Project 2004/217.20.
Objectives 1.
To identify potential protective antigens from N.pemaquidensis
using a combined DNA/protein approach.
2.
To identify and characterise attachment molecules involved in the
Outputs infection process of Atlantic Salmon by N.pemaquidensis.
3.
To demonstrate protection of Atlantic salmon against clinical AGD via cDNA and/or recombinant protein vaccination.

Characterisation of proteins involved in AGD pathogenesis including both attachment molecules and antigens that are differentially expressed during in vivo growth, but not in vitro.

A cDNA vaccine including a set of six antigen clones provided a relative increase in survival of approximately 40% and significant reductions in crude AGD Gill Scores were observed in field trials.

The vaccine significantly reduced both the crude gill score (visual percentage of gill surface affected by the parasite) and percentage of affected filaments in Atlantic Salmon challenged with acute AGD infection.

Further research is required on: assessing the crude vaccine under a chronic infection challenge in the sea under commercial growing conditions; refinement of the existing six-clone vaccine and additional antigens that may increase efficacy; optimisation of the delivery vector; potential protection when using protein vaccination; the nature of the response to the six antigens; the optimum dose required; and timing of vaccination prior to seawater transfer.

Outcomes

The six-clone vaccine is protected by patents.

There was a further round of funding that included a series of sea trials.

Sea trials for the experimental vaccine showed that the vaccine was unreliable in the field and the protection offered was variable (Chris
Benefits
Prideaux, pers. comm., 2012).

It was concluded that the level of protection would not warrant widespread commercial use.

Significant progress towards an effective vaccine to help manage AGD; however, progress is now stalled.

Scientific capacity enhanced.
Project 2004/217.20: Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: development of an AGD vaccine: phase II
Project details
Organisation: University of Technology (Sydney)
Period: Jun 2004 to Jun 2008
Principal Investigator: Robert Raison
Rationale This project continued (as part of phase 2) of the investment made earlier in other projects (e.g. Project 2002/251) to develop a vaccine to help manage
AGD for Atlantic Salmon aquaculture. Freshwater bathing to manage AGD was costly and was limiting farming sites due to the need for freshwater.
Further, it was stressful to the fish.
Vaccine development was considered part of a multifaceted approach to develop short-, medium- and long-term solutions to the control of AGD; development of a sub-unit vaccine being the long-term approach of the overall research strategy. While a vaccine against AGD was considered a very attractive solution, it was still recognised as a high risk and long-term prospect.
This project was carried out in conjunction with Project 2004/217.
Objectives 1.
To identify potential protective antigens from N.pemaquidensis
using a
Outputs combined DNA/protein approach.
2.
To identify and characterise attachment molecules involved in the infection process of Atlantic Salmon by N.pemaquidensis
.
3.
To demonstrate protection of Atlantic salmon against clinical AGD via cDNA and/or recombinant protein vaccination.

The project increased knowledge of the complex array of glycans and glycoproteins expressed on the surface of infective Neoparamoeba.

Cell surface antigens associated with attachment of the parasite to host tissue and unique to infectious Neoparamoeba have been identified using monoclonal antibodies.
 Of particular importance is the discovery of an “immunosuppressive” component present within the high molecular weight glycoproteins from infective Neoparamoeba. This finding, together with an indication of a protective effect derived from the use of oil emulsion adjuvant alone, forms the basis of further experiments aimed at optimising vaccination strategies for AGD.

A panel of anti-Neoparamoeba monoclonal antibodies was developed.

Fifty of these are specific for infective parasites and they reveal that the majority of the antigens uniquely expressed on infective parasites are carbohydrate in nature. This panel of antibodies is available as a resource for further AGD research.

An unexpected outcome from the vaccination trial was the finding that injection of adjuvant alone resulted in a significant level of protection from
AGD. This suggests that innate immune mechanisms may play an important role in protecting susceptible fish from infection with
Neoparamoeba.
Outcomes

Sound basis and greater confidence to proceed with further experimentation in vaccine development.

However, later sea trials for the experimental vaccine showed that the
Benefits vaccine was unreliable in the field and the protection offered was variable
(Chris Prideaux, pers. comm., 2012).

It was concluded that the level of protection would not warrant widespread commercial use.

Significant progress towards an effective vaccine to help manage AGD; however, progress is now stalled.

Scientific capacity enhanced.
Project 2004/218: Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: molecular assessment of resistance to AGD in Atlantic salmon
Project details
Organisation: CSIRO Marine and Atmospheric Research
Period: Jun 2004 to Sept 2008
Principal Investigator: Nicholas Elliott
Rationale Costs associated with AGD are severely limiting further expansion and sustainability of the Tasmanian Atlantic salmon industry. One of the strategies to minimise these costs was associated with the selection of stock that are more resistant to infection. A more resistant stock along with even a partially effective treatment and vaccine would be of major benefit to the long-term sustainability of the industry.
In 2003 it had been recommended that a selective breeding program should be established as soon as practical. A major trait for inclusion in the program was resistance to AGD. Research in relation to understanding AGD resistance for use in selective breeding was ranked second to oral treatments in an industry survey of AGD priorities in June 2003.
Understanding variation to AGD at the molecular level would allow both improved understanding of the phenotypic variation (that will benefit other research areas) and identification of specific genetic markers that would allow faster genetic gains in resistance to be made in a selection program than would be possible via standard phenotypic selection alone.
Objectives 1.
To define the molecular events underlying the progression of clinical AGD within Atlantic salmon.
2.
To undertake a molecular assessment of the inherent genetic resistance to
AGD in Atlantic salmon.
3.
To identify molecular markers associated with AGD resistance for application in a selective breeding program.

Outputs

Extensive knowledge and understanding was gained on a molecular basis of AGD resistance.

The project completed the first comparison of genetic variation at a coding gene between the domesticated Australian Atlantic salmon and their ancestral Canadian population; results were also compared to that published for European populations. In contrast to previously reported variation at non-coding microsatellite loci, a high level of variation at the major histocompatibility (MH) genes was observed within the domesticated Australian population, and observed sequence diversity exceeded that reported for other cultured Atlantic salmon populations.

The association between MH polymorphism and severity of AGD infection was examined in 30 full-sibling families by acute challenge. An association was observed between specific alleles and genotypes and AGD severity, as measured by infected gill filaments. Although statistically significant, the small sample sizes available through the challenge system limited the results to being suggestive and warranting further investigation.
 A PhD thesis entitled “Molecular assessment of resistance to amoebic gill disease” was completed successfully by James Wynne.
Outcomes

AGD resistance was found to be a complex trait.

There was a difference in genetic response between individuals challenged to an acute or chronic AGD infection. This may however have reflected an innate and acquired response to AGD, again supporting the point that
AGD resistance is not a simple trait.

As AGD resistance is a polygenic trait, marker assisted selection requires a whole of genome approach rather than a candidate gene approach as originally proposed.

The outcome of this project was the development of a proposal to enhance the genetic gains in the industry selective breeding program for AGD resistance through marker assisted selection on a whole genome basis.

The selective breeding program has incorporated AGD resistance and is progressing well; there are two primary selection traits in the Salmon
Enterprises of Tasmania (SALTAS) selective breeding program, growth and AGD resistance.

The SALTAS program has demonstrated significant genetic gains in these two traits and the first commercial cohorts from the program went to sea in
2012 (Nick Elliott, pers. comm., 2012).

The knowledge produced in the project has been used indirectly by the breeding program as the fundamental knowledge on understanding AGD pathogenesis supported the program; confirmation of the presence of an innate acquired response supported the program’s quantitative findings that
Benefits
 there were two distinct AGD resistance traits to accommodate (Nick
Elliott, pers. comm., 2012).
Contribution to reduction in costs of AGD to industry via the SALTAS breeding program.
Project 2006/225: Aquafin CRC - SBT Aquaculture Subprogram: improving fish husbandry and performance through better understanding of the relationship of fish stress and health
Project details
Organisation: University of Tasmania
Period: Dec 2005 to Jul 2010

Principal Investigator: Barbara Nowak
Rationale Improved performance in the SBT aquaculture industry can be achieved through stress reduction and minimising mortalities. These issues are crucial for longer term holding, when the initial size of tuna will be smaller and the fish will be farmed for a longer time, increasing health risks to the tuna.
Tuna are hardy under current husbandry practices, and the industry experiences low mortality. The wild capture of immunocompetent 3–5 yr old fish is the main reason, however the short growout time and advances in farming technology have been significant factors. Despite its newness, the industry enjoyed healthy returns for the first 10 years.
Since 2002 there had been a significant fall in revenue with a consequent greater focus on all aspects of the industry and particularly stress impacts limiting production. Stress may cause economic costs to the tuna industry in lost growth and condition. As the quota places a limit to what biomass can be farmed each year, the option of longer-term holding is a priority to increase productivity. Then the role of stress and the influence of husbandry practices on fish health and production are even more important.
As each individual fish has high commercial value, there was a need to develop non-lethal indices for SBT monitoring. Predictive indices were anticipated being valuable for planning production and harvesting.
Objectives 1.
To investigate the relationship between husbandry practices and SBT performance (at the level of tow and pontoon).
Outputs
2.
To investigate development of nonlethal indices for SBT health and performance and assess their predictive value.
3.
To determine the relationship between SBT health, stress and fish performance (individual fish level).

The project increased understanding of the effects of tow conditions on
SBT performance.

An industry data base was developed that included information from four companies from 2003 to 2008 and which confirmed the effects of tow condition on mortality; a total of 73 tows and 290 transfers into holding cages are currently included in the database.

Tow conditions, in particular duration of the tow but also in 2003-2006 tow biomass, had a significant effect on fish performance, including week



6-10 mortalities.
Mortality can be due to husbandry practices, the location of the company site or quality of the caught fish (e.g. mortality being correlated with biomass of fish on tow, the number of days of the tow and speed of tow).
The effect of tow on fish was reflected by a peak in cortisol level in SBT sampled at average weight in comparison to wild fish and fish sampled at midseason.
The results of this project showed that the best method of non-lethal bloodsampling was by bleeding fish caught on a baited hook without anaesthesia.



Although the non-invasive measurement of cortisol to assess stress in fish has been shown to be technically possible, the current method employed for these studies required further investigation for use with SBT.
There was a high variability for all three stress indicators – cortisol, glucose and lactate making detection of any seasonal or annual patterns
 difficult.
SBT showed a high level of individual variability with regard to stress levels and parasite loads. No relationship could be detected between parasite loads and stress levels or stress levels and immune response.
Outcomes

This project directly benefits the SBT industry by contributing to the understanding of the effects of stress and health on SBT performance.

The project has provided the core for the development of an integrated
 operational database for the SBT industry.
The tow history database has already provided tangible benefits to

 industry. Elucidation of the influence of stocking density and duration/speed of tow on subsequent mortalities has supported the adoption of a reduction in numbers of fish transported in tow cages and an increased attention on the location and timing of fish capture to reduce tow durations.
The database also has been the catalyst for developing a more extensive husbandry focused database to which the majority of industry operators have expressed a desire to contribute.
Industry has strongly adopted the consequential remedial action of
 industry workshops had a significant role in facilitating such industry options.
Aquatic Animal Health research benefits were provided from this project
Benefits through industry workshops and the involvement of postgraduate students in the project.

Potentially enhanced growth rates and fish condition from improved practices that reduce stress and parasite loads.

Capacity built for industry and for aquatic animal health research.
Project 2008/234: ASBTIA: Investigation of causes of mortalities in farmed SBT – variation to project 2008/228
Project details potentially increased environmental parasite loads by relocating sites. In some cases relocations have been up to 20 to 30 km away and out into water of 35 m depth. The results disseminated in milestone reports and
Organisation: University of Tasmania
Period: Feb 2009 to Dec 2009
Principal Investigator: Barbara Nowak
Rationale In the two years preceding this project, the SBT industry had experienced an increase in mortalities resulting in direct losses. In addition, SBT production had incurred changes in product quality associated with variable condition index and growth appears to have been compromised. It was estimated that the combined effect of all these production issues was costing the industry approximately $25m per annum.
The previous project in this cluster (2006/225) had demonstrated that SBT subjected to stress had significantly increased levels of copepods (mostly

Caligus chiastos ) and blood fluke ( Cardicola forsteri) in some ranching pontoons. Recorded infection levels in some experimental SBT had increased significantly from previous research levels by up to 4 times for blood fluke and 10 times for copepods. Although not present in season 2008, a ciliate that causes SBT mortality (swimmers disease) Uronema nigricans can have an adverse effect on SBT production by causing mortality in infected fish, generally at the later stage of growout.
The SBT industry continued to experience an upward trend in mortality, with one investigation suggesting the blood fluke Cardicola forsteri as a cause and an increase in the numbers of copepods and a relationship between the high number of copepods and low condition index had also been reported.
However, the exact cause or causes of mortalities have not been identified. It was possible that a combination of factors was needed to cause the mortalities.
There was a need to define the primary cause of the death as well as the contributing factors to be able to reduce SBT mortalities.
Objectives 1.
To investigate causes of mortalities of farmed SBT in 2009, in particular 6-
12 weeks mortalities.
Outputs
2.
To suggest preventative measures and/or further research to reduce mortalities in the future.

Uronema nigricans (swimmer syndrome) was the confirmed cause of mortality of 6.5% of the total number of moribund and dead fish.

However, it was likely that there were multiple causes of morbidity including tow-related factors.

Mortalities and moribund SBT had a lower condition index than control
 fish at all sampling times, suggesting that either the cause of death was chronic, or it had a lethal effect only on compromised fish.
Mortalities and moribund fish did not appear to be able to osmoregulate and maintain the balance of salt in their blood, however it was unknown if this contributed to the death or if it was a part of the death process.

The project provided training to ASBTIA staff, SBT industry and research students.

Future research priorities were proposed.
Outcomes

This project has increased the understanding of the causes of mortalities in

 ranched SBT.
Results of the project have been widely disseminated throughout the SBT industry through industry meetings, and workshops.
Improved focus for further research with priority given to experiments focussing on blood fluke; studies at pontoon level not individual fish; comparison of pontoons with high and low mortality, sampling live fish instead of mortalities, further analyses of SBT industry wide data; definition of tow and annual variation of health of wild fish regarding SBT performance.
Benefits


Lowered morbidity and improved status of health of SBT.
Capacity built for SBT industry and for aquatic animal health research.

2001/200
2001/205
2002/251
2003/225
2004/085
2004/213
2004/214
2004/215
2004/217
2004/217.20
2004/218
2006/225
2008/234
Total
The following tables show the annual investment by project for both the FRDC (Table 3) and for researchers and other investors (Table 4). Table 5 provides the total investment by year from both sources.
Table 3: Investment by FRDC by Project for Years Ending June 2002 to June 2010 (nominal $)
Project 2002 2003 2004 2005 2006 2007 2008 2009 2010 Total
2001/200
2001/205
2002/251
2003/225
2004/085
2004/213
2004/214
2004/215
2004/217
2004/217.20
2004/218
2006/225
2008/234
Total
93,314
97,194
0
0
0
0
0
0
0
20,564
72,783
86,932
139,539
43,181
88,529
60,998
-9,995
0
0
0
0
0
0
63,090 76,801 144,376 31,545 0 0
0 270,468 157,284 142,102 102,655 30,000
0
0
0 105,033 -13,511 40,440 -5,960
0
0
0
0 144,421 25,087 10,374 -29,980 49,967
0 -25,193 35,038 36,361 20,975 16,796
0 -72,603 160,678 101,457 39,913 7,243
0
24,201
0 0 87,295 8,483 123,523 -18,972 0
0
0
0
0
0
0
0
0
0 62,712 84,043 24,776 19,312
0 27,790
0
0
0
0
-2,808
65,346
0
8,954
35,312
0
-7,121
196,387
0
0
15,605
112,694
14,256
0
0
159,293
57,022
190,508 426,905 467,293 922,611 543,612 287,867 183,665 216,723 216,315
0
0
0
0
0
0
0
0
0
Source: FRDC project management database
Table 4: Investment by Researchers and Others by Project for Years Ending June 2002 to June 2010
Project 2002 2003 2004 2005
(nominal $)
2006 2007 2008 2009 2010 Total
304,989
388,050
315,812
702,509
126,002
199,869
83,977
260,889
200,329
190,843
42,420
569,032
71,278
3,455,999
225,088 49,603 209,693
226,814 245,615 213,935
0 49,498 60,255
0
0
0
0
0
0
0
0
0
0
175,770
0
0
0
0
104,159
0
113,272
102,214
48,625
145,714
105,731
100,620
147,136
0
24,749
92,348
49,877
154,709
82,118
116,449
0
0
0
0
0
0
66,713 19,496
0
126,990
91,993
0
0
0
118,325 119,781
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
735,679
686,364
247,774
456,541
98,502
427,413
279,842
455,175
0
0
0
0
0
0
0
0
0
0
0
0
200,229
255,000
75,202
0
237,519
254,908
67,399
95,118
217,516
230.947
65,191
290,091
0
0
0
275,770
0
0
0
149,691
0
0
0
77,046
655,264
740,855
207,792
887,716
0 0 0 0 0 0 0 88,569 0 88,569
451,902 520,486 735,342 1,257,981 1,248,694 1,162,005 275,770 238,260 77,046 5,967,486
Source: FRDC project management database
Table 5: Annual Investment in Cluster (nominal $)
Year ending
June
2002
2003
2004
2005
2006
2007
2008
2009
FRDC
190,508
426,905
467,793
922,611
543,612
287,867
183,665
216,723
Researchers and Others
451,902
520,486
Total
735,342 1,203,135
1,257,981
1,248,694
1,162,005
275,770
238,260
642,410
947,391
2,180,592
1,792,306
1,449,872
459,435
454,983

2010
Total
216,315
3,455,999
77,046 293,361
5,967,486 9,423,485
The investment in the 13 projects addressed fish health issues in both the Atlantic Salmon and SBT aquaculture industries. Table 6 summarises the major benefits by category delivered by each project.
Table 6: Category of Potential Benefits Delivered by Projects
Project Code and Brief Title Benefit
Reduced impact of AGD in
Atlantic Salmon via improved management and breeding
Potentially reduced impact of
AGD in Atlantic
Salmon via vaccine development
Improved SBT health and disease management
Enhanced research capacity
2001/200: Tuna cell line development
2001/205: Treatment and pathophysiology of AGD
2002/251: Development of a vaccine for AGD
2003/225: Farming practices and SBT health
2004/085: Detection of SBT pathogens
2004/213: Commercial AGD and salmon health project
2004/214: Effects of husbandry on AGD
2004/215: Establishment of challenge for AGD
2004/217: Development of an AGD vaccine: phase II
2004/217.20: Development of an AGD vaccine: phase II
2004/218: Molecular assessment of resistance to AGD
2006/225: Better understanding of the relationship of SBT stress and health


























2008/234: Causes of mortalities in farmed SBT
 
Summary of Potential Benefits
Economic
The principal economic benefit from these investments is a contribution to an actual/expected reduction in control costs and productivity losses in the Atlantic Salmon and SBT aquaculture industries. These potential benefits are likely to arise from management and breeding improvements in the case of Atlantic Salmon and from management improvements in the case of SBT. Despite the significant investment, no benefits are likely to emerge from the AGD vaccine development effort.
Environmental
The transport and use of large quantities of fresh water to the farming sites for fish washing purposes for control of AGD does create noise for nearby residential areas. If the investments in alternative
AGD control methods (e.g. breeding) in Atlantic Salmon aquaculture result in a reduction in the need for freshwater for washing fish, this will reduce the noise level for nearby communities.
Social
Capacity building benefits from the investments have been contributed by both formal and informal training characterised by most of the projects. This will benefit both the industries and the national research effort. Also, alternative control methods to washing fish may reduce stress and mortality with associated animal welfare benefits.
Table 7 provides in a triple bottom line framework a summary of the principal types of benefits associated with the outcomes of the investment.

Economic
Table 7: Summary of Potential Benefits in a Triple Bottom Line Framework
1. Reduced impact of AGD via improved management
Environmental
4. Potential for reduced noise impact of fish washing to remove AGD and carting fresh water to pontoons
Social
5. Enhanced research capacity
2. Potential future reductions in impact of AGD via resistance breeding
3.Improved SBT health and stress management
6. Reduced fish stress and enhanced animal welfare for both Atlantic
Salmon and SBT
The benefits identified above (1 to 6) have been classified into subjective beneficiary categories and a subjective estimate of their magnitudes is presented in Table 8.
Table 8: Categories of Benefits from the Investment
Fishing industry Spillovers
Other industries
Public
Economic
Environmental
1. *
2. **
3. ***
4.
*
Social 5. *
***Major contribution **Some contribution *Minor contribution
5. *
6. *
Public versus Private Benefits
Both private and public benefits will arise from the investment. On the basis of the distribution of the six benefits as classified by beneficiary in Table 8, and equal weighting for each benefit, it could be concluded that public benefits to Australia could make up only 40% of the total benefits. If the subjective weightings are taken into account, the public benefits would make up only about 30% of the total benefits.
Distribution of Benefits Along the Supply Chain
The private benefits and costs from a reduction in health/stress impacts from salmon and tuna would mainly be captured by aquaculture producers. However, these costs and benefits will be shared to some extent along the supply chain, including with seafood consumers.
Benefits to Other Industries
It is likely that most benefits will be confined to the aquaculture industry.
Benefits Overseas
As other countries farming Atlantic Salmon are subject to AGD impacts, it is likely that some benefits could accrue to those industries.
Additionality and Marginality

If FRDC had not received funding from government, most of these investments would probably still have been supported by FRDC and industry as they were highly relevant to improving productivity in the two principal aquaculture industries in Australia. The minor public benefit spillovers identified are therefore most likely to have been delivered without public investment. Further detail is provided in
Table 9.
Table 9: Potential Response to Reduced Public Funding to FRDC
What priority were the projects in this cluster when funded?
High
Would FRDC have funded this cluster if only half of public funding of FRDC had been available?
Yes, but with a lesser total investment (75% -
100%) of actual total investment and assuming industry levies remained the same.
Would the cluster have been funded if no public funding for FRDC had been available?
Yes, but with a lesser total investment (50% -
75%) of actual total investment
Match with National Priorities
The Australian Government’s national and rural R&D priorities are reproduced in Table 10 (updated in May 2007 and still current. http://www.daff.gov.au/_media/documents/ag-food/innovation2/Priorities_Booklet_FINAL.pdf
Table 10: National and Rural R&D Research Priorities
Australian Government
National Research Priorities
1. An environmentally sustainable Australia
2. Promoting and maintaining good health
3. Frontier technologies for building and transforming Australian industries
4. Safeguarding Australia
Rural Research Priorities
1.Productivity and adding value
2. Supply chain and markets
3. Natural resource management
4. Climate variability and climate change
5. Biosecurity
Supporting the priorities:

Innovation skills

Technology
The projects contribute to National Research Priority 3 (Frontier technologies) and to Priority 4
(Safeguarding Australia). The investment was strongly associated with Rural Research Priorities 1, 2 and 5. Both supporting priorities also were addressed.
Benefits Valued
Three benefits are valued in this cluster of projects:

Reduction in future production costs of Atlantic Salmon due to management improvements impacting on AGD.

Reduction in future production costs of Atlantic Salmon due to AGD resistance being delivered via the breeding program

Enhanced productivity in the SBT industry
Benefits not Valued
The benefits identified but not valued are:

 the enhanced research and scientific capacity built due to the investments
 the potential for noise reduction due to improved (non washing) methods of AGD control.
 the animal welfare benefits
Reasons for these benefits not being valued included the difficulty of valuation of the different scientific capacities developed and the lack of readily available evidence to support assumptions for the noise and animal welfare benefits.
Benefits 1 and 2: AGD cost reductions
Costs of AGD
Atlantic Salmon production in Tasmania continues to increase as is shown in Table 11. Over the five years ending June 2006 to 2010, the average annual production has been 25,518 tonnes and the average annual value has been $13,000 per tonne.
Table 11: Tasmanian Salmonid Production and Value 2006-2010
Year ended June Production
Value ($’000)
Value ($/tonne)
2006
(tonnes)
19,219 356,000 18,523
2007
2008
2009
23,975
24,428
29,016
281,710
293,134
319,175
11,750
12,000
11,000
2010
Average
30,950
25,518
362,422
322,488
11,710
12,997
Source: ABARES, 2011
Estimates of the cost of AGD to the salmon industry vary between $20 and $50 million per annum due to the vast amount of freshwater required as well as significant amounts of additional labour. For example, Huon Aquaculture report that of 100 people employed on their farms, 60 are involved in freshwater bathing and support infrastructure (Austasia Aquaculture, 2011).
An estimate of the current cost of AGD to the industry of $50 m has been provided by the Tasmanian
Salmonid Growers Association Ltd (Adam Main, pers. comm., 2012). Another estimate supported
$50 m but acknowledged the cost was difficult to quantify (Steve Percival, pers. comm., 2012). A lower estimate of both control costs and productivity losses is $20-25 m per annum (Aquafin CRC,
2008, p 28), but this estimate was made a few years ago and the industry size and value has increased since that time. Taking these three estimates into account, a conservative estimate of $40 m per annum is used in the current analysis.
The eight projects in the cluster that address AGD have resulted in new knowledge, increased understanding and refined research techniques. The prospective benefits have been divided into potential short-term benefits (Benefit 1) from improved management and longer-term potential benefits (Benefit 2) from building resistance via breeding.
Benefit 1: Management improvements
Some important findings have been delivered but with no changes or only minor management cost implications (Adam Main, pers. comm., 2012; Steve Percival, pers. comm., 2012). The cost reduction via management changes due to the investment is estimated as a maximum of 2% for those improving, with adoption at 50% of the industry and with benefits beginning in 2011 and reaching the maximum of 2% of costs five years later.
Benefit 2: Breeding improvements

The development of resistance to AGD via the breeding program is still ongoing. It is assumed that the probability of the research being successful in building some resistance into salmon lines is 80% by 2018. The development of resistant lines is expected to reduce the overall cost of AGD to the industry by 25% by 2018. The first releases from the breeding program went to sea in 2012 and will be expected to be harvested in 2013.
It may take some time for the industry to change their management protocols to reduce washing, but reduced mortality and improved feed conversion ratios should result in productivity gains in the shorter term (Nick Elliott, pers. comm., 2012). Hence the cost reduction is assumed to commence in
2014 at 5% and increase linearly to 25% by 2018.
The resistance benefit via breeding is assumed to be additive to the cost reduction of 2% due to other management improvements outlined earlier.
Attribution
The investment covered in this cluster was only a sub-set of the total research effort devoted to AGD over the period 2001 to 2012. The cluster covers 8 projects out of 17 related to AGD (Source: FRDC database). Further there has been, and there will be, additional non-FRDC projects that have contributed or will contribute in future to the estimated benefits.
Hence, only 40% of the management benefits estimated and 20% of the breeding benefits have been attributed to the investments in the cluster. A detailed summary of all assumptions made for both management and breeding benefits is provided in Table 13.
Benefit 3: Costs and Productivity of Southern Bluefin Tuna (SBT)
Farmed SBT production in Australia has remained fairly stable in the last five years as shown in Table
12. Over the five years ending June 2006 to 2010, the average annual production has been 8,424 tonnes and the average annual value has been $17,400 per tonne.
Table 12: South Australian Farmed SBT Production and Value 2006-2010
Year ended June Production Value ($’000) Value ($/tonne)
(tonnes)
2006 8,806 155,795 17,692
2007
2008
2009
7,486
9,757
8,786
137,650
186,742
157,777
18,388
19,139
17,958
2010
Average
7,284
8,424
102,175
148,028
14,027
17,441
Source: ABARES, 2011
Industry costs of SBT relating to health and disease
Project 2008/234 reports that production issues related to mortality and product quality associated with variable condition index and growth was costing the industry $25 m per annum. This estimate was supported by SARDI’s Marty Deveney (pers. comm., 2012) who suggested this may be for an average year with reported annual losses of $40-50 m on occasion due to high mortality levels.
Another estimate is that industry mortality reached a peak of 13% in 2010 and has since dropped to below 2% in 2012 (David Ellis, pers. comm., 2012). Based on mortality alone and a gross value of production of $200 m the cost in 2010 would have been approximately $26 m. In addition to mortality there are impacts on growth and product quality not included in this total. The drop in mortality to 2% was largely due to Project 2008/228 resulting in blood fluke treatments (David Ellis, pers. comm.,
2012). However, Project 2008/228 was not included in the cluster being analysed (as it had not been completed).

Cost reduction
As a result of the findings of projects in the cluster, an improved understanding of the effects of stress and health on SBT performance has eventuated. Also some associated practice changes have been made by some parts of the industry (e.g. relocating sites, stocking density, feeding practices). Project
2008/234 also led to Project 2008/228 where blood fluke treatment methods were developed; in turn these have significantly reduced mortality levels as mentioned earlier. Treatment of blood fluke has lowered mortality by 90% on some farms and they have now been reporting less than 2% mortality for the past two years (Marty Deveney, pers. comm., 2012).
Overall, the change in practices and are assumed to have averted some 10% of the annual costs due to improved understanding and management and but including only a small part of the total benefit from improved blood fluke management. However, all of the SBT projects included in the cluster have played a role in the significant outcomes delivered by Project 2008/228, for example, by providing greater understanding and identifying further research priorities (David Ellis, pers. comm., 2012).
The 2008/228 success was because many researchers, government agencies and industry personnel were involved in a collaborative effort to solve health issues so delivering rapid extension of results
(David Ellis, pers. comm., 2012). Also, such inputs from the Aquafin CRC’s work on physiology and metabolism provided an insight into how blood fluke was impacting on the cardiovascular system of
SBT (David Ellis, pers., comm., 2012).
It is assumed that the cost reduction first commenced in 2011 and will take five years to reach its maximum of 10% in 2015. This 10% would have been much higher if Project 2008/228 had been included in the cluster.
Attribution
The investment covered in this cluster was only a sub-set of the total research effort and other factors such as industry innovation and management devoted to health and stress issues in SBT. Hence, only
40% of the benefits estimated have been attributed to the projects analysed.
Summary of Assumptions
A summary of the key assumptions made is shown in Table 13.
Table 13: Summary of Assumptions
Assumption Source Variable
Atlantic Salmon: AGD Costs
Annual impact of AGD without research
$40 m per annum Estimate based on
Aquafin CRC (2008) and discussions with Adam
Main of Tasmanian
Salmonid Growers
Association (TSGA) and
Steve Percival of Huon
Aquaculture
Atlantic Salmon : Management benefits
Reduction in annual impact of 2% of existing AGD costs
AGD with management changes
(treatment cost reduction plus productivity losses saved)
Maximum adoption level 50%
Agtrans assumption after discussions with Adam
Main of TSGA
Agtrans

Proportion of expected benefits attributable to projects in cluster
40%
First year of benefits
Year of maximum benefits
2010/11
2014/15
Atlantic Salmon: Potential Breeding Benefits
Reduction in annual impact of 25% of existing AGD costs (less
AGD with successful resistance built from breeding frequent washing required plus productivity gains)
Probability of impact occurring 80% by 2018
Year of first benefit 5% in 2014
Agtrans estimate, after consideration of associated AGD expenditure
Agtrans estimate
Agtrans estimate
Elliott (2011)
Year of maximum benefit 25% in 2018
Agtrans Research
Based on first cohort release
Agtrans Research, based on discussions with Nick
Elliott
Agtrans Research Maximum expected benefit to industry in 2018
Proportion of benefits attributable to projects in cluster
$40m * 25% * 80% = $8m pa
20% Agtrans estimate, after consideration of previous
FRDC expenditure
Farmed Bluefin Tuna – Stress and Productivity Management
Annual cost of stress and $25 m per annum in 2010 productivity losses for SBT without research investment
10% of 2010 impact Reduction in cost of impact due to investment
Proportion of benefits 40% attributable to projects in cluster
FRDC Project 2008/234 and input from Marty
Deveney and David Ellis
Agtrans assumption
First year of benefits
Year of maximum benefits
2010/11
2014/15
Agtrans estimate, after consideration of other
R&D investment and industry innovation and management
Agtrans estimate
Agtrans estimate
All past costs and benefits were expressed in 2010/11 dollar terms using the CPI. All benefits after
2010/11 were expressed in 2010/11 dollar terms. All costs and benefits were discounted to 2010/11 using a discount rate of 5%. The base run used the best estimates of each variable, notwithstanding a high level of uncertainty for many of the estimates. Investment criteria were estimated for both total investment and for the FRDC investment alone. All analyses ran for the length of the investment period plus 30 years from the last year of investment (2009/10) to the final year of benefits assumed .
Tables 14 and 15 show the investment criteria for the different periods of benefits for both the total investment and the FRDC investment.
Table 14: Investment Criteria for Total Investment for Different Periods of Benefits
(discount rate 5%)
Investment criteria Years since last year of investment
Present value of benefits ($m)
Present value of costs ($m)
0
0.00
14.72
5 10 15 20 25 30
3.86 12.95 20.66 26.69 31.42 35.12
14.72 14.72 14.72 14.72 14.72 14.72

Net present value ($m)
Benefit–cost ratio
Internal rate of return (%)
-14.72
0.00
-10.86
0.26
Negative Negative
-1.77
0.88
3.8
5.93 11.97 16.70 20.40
1.40 1.81 2.13 2.39
7.6 9.1 9.8 10.2
Table 15: Investment Criteria for FRDC Investment for Different Periods of Benefits
(discount rate 5%)
Investment criteria
Present value of benefits ($m)
Present value of costs ($m)
Net present value ($m)
Benefit–cost ratio
Internal rate of return (%)
0
0.00
5.39
-5.39
5
Years since last year of investment
1.42
5.39
-3.98
0.00 0.26
Negative Negative
10
4.75
5.39
-0.65
0.88
3.8
15
7.57
5.39
2.18
1.40
7.6
20
5.39
4.39
1.81
9.1
25 30
9.78 11.52 12.87
5.39
6.12
2.14
9.8
5.39
7.48
2.39
10.2
The annual cash flow of undiscounted benefits is shown in Figure 1 for both the total investment and for the FRDC investment.
3.00
2.50
2.00
1.50
1.00
0.50
0.00
Total
FRDC
Years
Figure 1: Annual Cash Flow of Benefits
The present value of benefits (PVB) from each benefit source was estimated separately and then summed to provide an estimate of the total value of benefits. Table 16 shows the sources of benefits, expressed as the PVB and the percentage of total benefits.
Table 16: Source of Benefits (discount rate 5%, 30 year period)
Benefit % Total
6.5
53.0
PVB
($m)
2.28 Atlantic Salmon : Management
Atlantic Salmon: Breeding
Farmed SBT: Stress and Productivity Management
Total
40.5
100.0
18.61
14.23
35.12
Table 17 shows a subjective assessment of the different benefits against the rural research priorities.
Bear in mind that this assessment refers only to those benefits that were valued.

Benefit
AGD Cost savings from management
AGD cost savings breeding development
SBT cost savings
Total ($m)
Table 17: Benefits Valued and Rural Research Priorities
PVB
($m)
Product ivity and
Adding
Value
Supply
Chain and
Markets
Natural
Resource
Manage ment
Climate
Variability and
Climate
Biosecurity
Change
% subjective allocation to each priority
2.28 50% 10% 0% 0% 40%
18.61
14.23
35.12
50%
50%
17.56
10%
10%
3.51
0%
0%
0
0%
0%
0
40%
40%
14.05
Total (%) 100 50% 10% 0% 0% 40%
Sensitivity Analyses
Sensitivity analyses were carried out on some variables and results for the total investment are reported in Tables 18 to 19. All sensitivity analyses were performed with benefits taken over the life of the investment plus 30 years from the year of last investment. All other parameters were held at their base values.
The sensitivity analysis on the discount rate (Table 18) demonstrates that the investment criteria of net present value and benefit cost ratio are sensitive to the discount rate.
Table 18: Sensitivity to Discount Rate
(Total investment, 30 years)
Criterion
Present value of benefits ($m)
Present value of costs ($m)
Net present value ($m)
Benefit-cost ratio
Discount Rate
0% 5% (base) 10%
72.48
11.13
61.35
6.51
35.12
19.93
14.72
19.38
20.40
0.55
2.39
1.03
The sensitivity analysis on the cost reductions (Table 19) demonstrates that even if all the cost reduction estimates are halved, the investment still breaks even at the 5% discount rate.
Table 19: Sensitivity to Cost Reductions Assumed
(Total investment, 30 years)
Criterion Maximum Cost Reduction for Salmon Management,
Salmon Breeding and SBT Productivity
Present value of benefits ($m)
Present value of costs ($m)
Net present value ($m)
Benefit-cost ratio
1%, 12.5% and
5% (Pessimistic)
17.56
14.72
2.84
1.19
2%, 25% and
10% (Base)
35.12
14.72
20.40
2.39
4%, 50% and
20% (Optimistic)
70.25
14.72
55.53
4.77

Internal rate of return (%) 6.0 10.2
15.0
Confidence Rating
The results produced are highly dependent on the assumptions made, many of which are uncertain.
There are two factors that warrant recognition. The first factor is the coverage of benefits. Where there are multiple types of benefits it is often not possible to quantify all the benefits that may be linked to the investment. The second factor involves uncertainty regarding the assumptions made, including the linkage between the research and the assumed outcomes.
A confidence rating based on these two factors has been given to the results of the investment analysis
(Table 20). The rating categories used are High, Medium and Low, where:
High: denotes a good coverage of benefits or reasonable confidence in the assumptions made denotes only a reasonable coverage of benefits or some uncertainties in assumptions Medium: made
Low: denotes a poor coverage of benefits or many uncertainties in assumptions made
Table 20: Confidence in Analysis of Cluster
Coverage of Benefits
Medium
Confidence in
Assumptions
Medium
Observations for future investment and evaluation include:
The FRDC project management system was found valuable in being able to extract funding information by financial year across a range of individual R&D areas. However, an improvement would be if an annual time series for R&D expenditure within individual R&D areas could also be made available. This would also be helpful to FRDC for tracking and reporting R&D investment across areas over time.
As with other clusters, final reports and technical summaries were not always easy to find in the related documents section of the data base. It would be helpful to the evaluation effort if there was a separate field containing the final report and the technical summary (separately) to assist with time savings and ensuring the correct report is located.
The ratio of FRDC funding to total funding for FRDC projects in this cluster was 37 (FRDC) to 100
(total) or 37%. This was close to the average percentage of 40% found for 18 clusters in 2009.
It would be of value to economic assessments such as this if industry information on disease costs, including treatment, mortality, and productivity losses could be monitored over time. As well as aiding evaluation of past research, such information may be useful in priority setting for future research.
The two Theme 1 key performance indicators are described in Table 21.
Table 21: Key Performance Indicators for Theme 1
KPI Description
1 Development and dissemination of protocols,
Number of projects contributing
13

2 techniques and technologies to mitigate and minimise the impact of disease outbreaks
Development of knowledge to assist industry to register vaccines and veterinary chemicals.
4
All 13 projects were considered to have contributed to KPI 1. Four projects contributed also to KPI 2.
Investment was made in a total of 13 projects within the cluster with the FRDC contribution approximating 37% of the total costs of investment. Of the 13 projects in the cluster, 8 projects were relevant to the Atlantic Salmon and 5 to SBT.
On the basis of the distribution of the six benefits as classified by beneficiary in Table 8, and equal weighting for each benefit, it could be concluded that public benefits to Australia could make up 40% of the total benefits. If the subjective weightings are taken into account, the public benefits would still make up 30% of the total benefits.
The principal benefits valued from this cluster of projects were reduced costs in treating AGD in
Atlantic Salmon (predominantly from the resistance breeding initiative to which the cluster contributed to some degree) and averted productivity losses in SBT.
Project 2008/228 has been lauded by industry as averting significant mortality in SBT. The SBT benefits valued in the current analysis would have been significantly greater if the full benefits from improved management of blood fluke could have been attributed to the investments included in the cluster. Project 2008/228 was not included in the cluster as it was not completed when the cluster was defined.
Overall, the investment criteria estimated for the total investment of $14.7 million (present value of costs) in the cluster were positive with a present value of benefits of $35.1 million, a net present value estimated at $20.4 million, and a benefit-cost ratio of 2.4 to 1, all estimated using a discount rate of
5% (benefits estimated over 30 years from the final year of investment).
Nathan Bott, South Australian Research and Development Institute (SARDI)
Marty Deveney, SARDI
David Ellis, Australian Southern Bluefin Tuna Industry Association
Nicholas Elliott, CSIRO
Kathy Ophel–Keller, SARDI
Adam Main, Tasmanian Salmonid Growers Association Ltd
Steve Percival, Huon Aquaculture
Chris Prideaux, CSIRO
ABARES (2011) “Australian Fisheries Statistics 2010”, Canberra.
Aquafin CRC (2008) “Achievements and Impacts (2001-2008), Adelaide http://www.sardi.sa.gov.au/__data/assets/pdf_file/0007/91744/Final_Aquafin_CRC_achieve ments_booklet_08.pdf
Austasia Aquaculture (2011) “The Worlds Best Salmon”, Autumn 2011, p4.
Elliott N, King H, Kube P, Taylor R and Evans B (2011) “Breeding Program for Tasmanian Salmon:
Partnership using DNA Genotyping to Reduce AGD Treatments”, Global Aquaculture
Advocate, March /April.
FRDC (2010) “Investing for tomorrow’s fish: the FRDC’s Research, Development and Extension
Plan 2010–2015”, FRDC http://www.frdc.com.au/research/current-plan