SCRC: PhD 6.06 – Capturing And Maintaining Genetic Variation When Initiating Selective Breeding Programs For Aquaculture
Funder
Fisheries Research and Development Corporation
Summary
Industry need: The following projects have stated the need for establishing sustainable selective breeding programs; • Development of a genetic management and improvement strategy for temperate marine finfish (2008/723). • Scope and economic analysis of options for a nationally unified breeding program for abalone aquaculture (2008/722). • Development of a genetic management strategy for cultured Barramundi (2008/758).
Seafood CRC: Promoting Marine Finfish Aquaculture In NSW
Funder
Fisheries Research and Development Corporation
Funding Amount
$99,990.13
Summary
NSW currently imports over 85% of its seafood and needs a substantial increase in investment and production, most notably, major new marine based aquaculture development.(Bond University, 2012). However, marine aquaculture development is fundamentally constrained by the lack of background biological and economic information. To promote marine finfish production, the NSW government has invested significantly in establishing, through the normal application pathway (EIS, REF, public consultation, D ....NSW currently imports over 85% of its seafood and needs a substantial increase in investment and production, most notably, major new marine based aquaculture development.(Bond University, 2012). However, marine aquaculture development is fundamentally constrained by the lack of background biological and economic information. To promote marine finfish production, the NSW government has invested significantly in establishing, through the normal application pathway (EIS, REF, public consultation, DA), a 20 ha Marine Aquaculture Research Lease (MARL) off Port Stephens with approval to produce up to 300 t fish/annum. The MARL is a vehicle to streamline approvals process, foster the social licence required for finfish production expansion in NSW, and to provide the fundamental information needed to encourage investment.
There are three key end users for MARL research: Industry, Public and Regulators. The research proposed on the lease will address short term needs central to the development of fish farming in subtropical waters of the Australian east coast and develop a platform for ongoing research. DPI has begun dialogue with potential commercial partners to operate the MARL. These discussions have established that yellowtail kingfish (YTK) is the primary species of interest (although tuna is a candidate and is specifically approved for the MARL). This interest in YTK is in part is driven by a shortfall of Kingfish and Barramundi from aquaculture in local markets – of the order of 460 t at the Sydney Fish Market alone last financial year.
Industry need: YTK production within Australia has not been without its challenges and further research is essential, particularly when entering new farming environments. Previous CRC research (SFCRC 2008/903) has developed models showing rapid growth for YTK in warmer waters (<18 months to 4.5 kg), but these models need validation. Further, there is a need to investigate health challenges and potential management options in a new offshore environment.
Public need: In gaining approval for the MARL, extensive public consultation was undertaken that identified key concerns with respect to the sustainable operation of the MARL. Traditional concerns over nutrient enrichment arose but were overshadowed by issues related to potential impacts on species of sharks and cetaceans. There is a need to investigate the MARL interaction with these species, and Port Stephens is uniquely well placed for this to occur. Port Stephens has the most intensive cetacean watch industry in the world and is the focus of a juvenile white shark and grey nurse shark monitoring program.
Regulatory need: DPI is funding development of a Marine Waters Sustainable Aquaculture Strategy for NSW (MWSAS), under State Environmental Planning Policy 62 – Sustainable Aquaculture (SEPP62) to streamline investment pathways and promoting sustainable seafood production. A MWSAS will describe the approvals process, best practice system design and operation, and identify areas suitable for future development. MARL research will inform a MWSAS in key areas of sustainability Objectives: 1. To obtain background environmental data for MARL operation 2. To have commenced development of a Marine Waters Sustainable Aquaculture Strategy for NSW 3. To have established the validity of existing growth/nutrition and economic performance models for Yellowtail Kingfish and Mulloway 4. To have determined any health challenges for finfish production and consequent management options in an offshore environment Read moreRead less
Assessment Of Restriction Enzyme Analysis Mitochondrial DNA For The Identification Of Stocks Of Commercially Important Marine Species And For The Detection Of Genetic Markers For The Use In Salmonid Husbandry
Funder
Fisheries Research and Development Corporation
Funding Amount
$54,045.00
Summary
Objectives: 1. Collect tissue, extract DNA. Restriction enzyme analysis to mt DNA samples to (1) calculate genome similarity, apply to known population biology to describe genome dynamics in marine spp 2. (2) survey diversity rainbow trout & Atlantic salmon. 3. Can mtDNA genome be genetic marker?
Stock Delineation Of The Pink Ling (Genypterus Blacodes) In Australian Waters Using Genetic And Morphometric Techniques
Funder
Fisheries Research and Development Corporation
Funding Amount
$219,149.62
Summary
There are two basic needs for the ling fishery that are addressed by this proposal:
1) It is important to determine whether pink ling from WA, the GAB, the SEF Eastern sector, and the SEF Western sector represent separate stocks, with the implied need for a separate management plan for each, or are simply components of a single large stock best managed as a single entity. Industry has noted the potential for development of the fishery in the west. It is particularly important to establi ....There are two basic needs for the ling fishery that are addressed by this proposal:
1) It is important to determine whether pink ling from WA, the GAB, the SEF Eastern sector, and the SEF Western sector represent separate stocks, with the implied need for a separate management plan for each, or are simply components of a single large stock best managed as a single entity. Industry has noted the potential for development of the fishery in the west. It is particularly important to establish whether or not the developing western fishery is distinct from the more fully exploited eastern fishery. Stock delineation work needs to be carried out before reliable biomass and yield estimates of stocks can be derived, and before new management plans are put into operation.
2) It is necessary to know for certain whether the orange form is the juvenile pink ling or whether it is a distinct species. This is necessary to integrate non-trawl components of the fishery with the trawl component. If the orange form is the juvenile of the pink form, then it will be important to manage gear types, such as set-netting, that most affect the smaller orange ling. The lack of such protection may otherwise impact on recruitment to the deepwater part of the fishery, which represents almost all of the economic value of ling. Whilst preliminary allozyme analysis indicates that the two colour forms of ling are the same species, there is a need to confirm this using more powerful genetic techniques. Objectives: 1. Delineate stock structure of pink ling in Australian waters so that separate management plans for each stock can be developed if required. 2. Examine the nature and relationship of orange and pink forms of ling so that management plans for the deepwater and inshore components of the fishery can be properly integrated. 3. To collect biological information, particularly in regards to life history and reproduction, that can be used together with stock delineation results and other information to develop yield estimates so that TACs can be reviewed. Read moreRead less
Predicting Renal, Ophthalmic And Heart Events In The Aboriginal Community: The PROPHECY Diabetes Multi-Omics Cohort Study
Funder
National Health and Medical Research Council
Funding Amount
$3,955,505.00
Summary
Diabetes is at epidemic levels in Indigenous Australians, impairing quality of life, and contributing to poor health. This is a result of rapid development of kidney, heart and eye complications. We have established a large long-term population study among Aboriginal communities within South Australia and will explore the burden, natural history and the social, psychological, environmental, clinical and genomic predictors of diabetes and its complications.
Discovering sex determining genes in a reptile with genetic and environmental sex determination. Reptile sex determination is particularly fascinating because it is triggered either by genes on sex chromosomes or by the nest temperature. This project will identify and characterise candidate sex determining genes in a model reptile to understand how genes control sexual differentiation and how they interact with temperature.
Was an ancient bird-like sex chromosome system ancestral to reptiles and mammals? Recent discoveries reveal amazing similarity in the sex chromosomes of distantly related animals. This project will use advanced DNA technology to explore diverse sex chromosomes in reptiles to discover whether this signifies ancient and unsuspected common ancestry, or the convergent redeployment of genes and chromosomes predisposed to determine sex.
Patterns Of Interaction Between Habitat And Oceanographic Variables Affecting The Connectivity And Productivity Of Invertebrate Fisheries
Funder
Fisheries Research and Development Corporation
Funding Amount
$270,000.00
Summary
This study will provide a better understanding of the importance of scale relationships between benthic habitat, oceanography, and biology and their independent and interactive impact on larval dispersal, settlement and productivity in the Victorian blacklip abalone Haliotis rubra, and southern rock lobster Jasus edwardsii fisheries. Understanding the scale of these relationships is critical for spatial management in determining the sharing of responsibility between Government as the regulator a ....This study will provide a better understanding of the importance of scale relationships between benthic habitat, oceanography, and biology and their independent and interactive impact on larval dispersal, settlement and productivity in the Victorian blacklip abalone Haliotis rubra, and southern rock lobster Jasus edwardsii fisheries. Understanding the scale of these relationships is critical for spatial management in determining the sharing of responsibility between Government as the regulator and Industry as the lead for the implementation of voluntary and appropriately scaled management strategies.
Population dynamics, habitat availability, complexity, and physiography determining dispersal, settlement, survivorship and growth need to be considered in order to understand the primary drivers of productivity on local geographical scales, and the resilience of fishing stocks to fishing pressure and threats associated with environmental change, including pests and disease. Importantly, and pertinent to species such as southern rock lobster with prolonged planktonic larval phases, understanding these dynamics on broad spatial and temporal scales will assist in determining the dependency of Victorian fisheries on interstate recruitment sources.
These factors will be explored using a multidisciplinary approach involving geospatial, oceanographic and biophysical modelling, and genomic technologies providing industry with a framework for guiding future management decisions. Outputs from this study will provide industry with data and guidelines for assessing the resilience or vulnerabilities of specific fishing stocks to overharvesting or environmental disturbance, and the potential for natural replenishment in the event of stock depletion. Ultimately this will help guide where stock restoration and enhancement activities are needed to catalyse recovery, or where reef closures may be beneficial for recovery.
Objectives: 1. Integrate commercial catch and survey data with LiDAR-derived seafloor structure information to identify the spatial structure and patch-level productivity of reef systems,potential abalone fishable habitat extent and map important source reefs of abalone larvae. 2. Development of a high resolution hydrodynamic model for Victorian coastal waters that allows the modeling of larval dispersal between individual reef complexes throughout state waters. 3. Development of a biophysical larval dispersal model to map the probable dispersal pathways for H. rubra and SRL across Victorian reef complexes. 4. Determine if recruitment across the respective fisheries is influenced by adaptive genetic factors. Read moreRead less
Postgraduate Funding - Population Biology And Dynamics Of Yellowfin Whiting
Funder
Fisheries Research and Development Corporation
Funding Amount
$75,000.00
Summary
The South Australian Marine Scalefish Fishery (MSF) is the most complex fishery in South Australia and is currently undergoing transition through structural reform, development of new harvest strategies and review of the Management Plan. Changes in the dynamics of the fleet have resulted in redirection of effort from primary species such as garfish, snapper and King George whiting towards secondary species including yellowfin whiting.
Yellowfin whiting Sillago schomburgkii is the second ....The South Australian Marine Scalefish Fishery (MSF) is the most complex fishery in South Australia and is currently undergoing transition through structural reform, development of new harvest strategies and review of the Management Plan. Changes in the dynamics of the fleet have resulted in redirection of effort from primary species such as garfish, snapper and King George whiting towards secondary species including yellowfin whiting.
Yellowfin whiting Sillago schomburgkii is the second most valuable Sillaginid after King George whiting and one of the most valuable secondary species in the MSF fishery with most catches from Northern Spencer Gulf, and smaller catches from the West Coast, Southern Spencer Gulf, and Gulf St Vincent. There are also significant recreational catches (31.5% of State catch in 2013/14).
There is a need for improved understanding of the life-history of yellowfin whiting with quantitative estimates of population dynamics including reproduction, growth performance and stock structure. Oceanographic separation of Spencer Gulf and Gulf St Vincent suggests that yellowfin whiting may constitute separate stocks in these regions while possible population sub-structuring occurring at smaller scales has implications for fishery management. There is potential to compare results of the proposed study with previous work to investigate whether decadal changes in the demography and population dynamics of yellowfin whiting have occurred in the South Australian Gulfs, as well as potential factors driving any change.
This project proposal aims to (i) build the capacity for scientific investigation of finfish species in South Australia by providing an opportunity for a science graduate to develop skills in fishery science, (ii) improve the understanding of life-history and population dynamics of yellowfin whiting, and (iii) improve understanding of the stock structure of yellowfin whiting. This project will have linkages to another FRDC funded project (2017/023), “ESD risk assessment for under-utilised species to facilitate structural reform of South Australia’s commercial Marine Scalefish Fishery”.
Objectives: 1. Define the stock structure of yellowfin whiting in South Australia and the relationship to Western Australian stocks using genomic approaches. 2. Define finer scale population structure of yellowfin whiting in the South Australian gulfs using otolith chemistry. 3. Examine spatial and temporal trends in catch among yellowfin whiting and other species in the marine scalefish fishery and how representation among different life-history strategy groups has changed. 4. Investigate size and age structures of yellowfin whiting in the two gulfs of SA and how these have changed over a 22 year period. 5. Increase fisheries science capacity in South Australia through training of the next generation of researchers. Read moreRead less
Assessment Of The Utility Of Genomics For Sydney Rock Oyster Breeding
Funder
Fisheries Research and Development Corporation
Funding Amount
$620,000.00
Summary
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 bre ....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. Objectives: 1. Collect tissue samples using non-lethal methods and tagging to identify oysters 2. Sequence the whole genomes of selected individuals at high read depth, which will serve as the genotype resource for the project 3. Identify the associations between genotypes and phenotypes and compile a list of genetic markers and the genes associated with QX survival, whole weight and meat condition to then use modelling (for genomic predictions) to give individuals breeding values Read moreRead less