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
Bringing The Iconic Australian Herring (Arripis Georgianus) To The Food Service And Retail Market – Phase One
Funder
Fisheries Research and Development Corporation
Funding Amount
$70,000.00
Summary
This Australian Herring FRDC project is a strategic initiative to promote the recently recovered commercial Herring fishery. Blueshift and the commercial sector – represented by Fins Seafood and Albany Seafoods, are strong supporters of benefiting the commercial herring industry through increased demand and production. Fins Seafood focus on locally sourced seafood and have the experience and are passionate in this area, solidifying their undeniable importance to be a part of this project. This Australian Herring FRDC project is a strategic initiative to promote the recently recovered commercial Herring fishery. Blueshift and the commercial sector – represented by Fins Seafood and Albany Seafoods, are strong supporters of benefiting the commercial herring industry through increased demand and production. Fins Seafood focus on locally sourced seafood and have the experience and are passionate in this area, solidifying their undeniable importance to be a part of this project.
The project is needed to reaffirm the presence Australian Herring within the seafood market as commercial landings increase over the coming decade. If Australian Herring is successfully marketed, there is a potential for success within the local domestic market and potentially for export, if export approval is granted by the Australian Government. Furthermore, it is designed to address these challenges by providing investment for research, development, and extension initiatives aimed at improving the sustainability and profitability of the Australian Herring fishery. If successful, this proposal aims to obtain an accurate sense of the market appetite and consumer demand, as well as the potential to value-add by using local seafood processors.
Effective marketing through potential branding, introduction of new products and developing the presence of Australian Herring locally will be beneficial to industry and consumers. Furthermore, successful utilisation of all associated fish waste will bring more value and benefit to industry.
Objectives: 1. Identification of the current market demand and future demand forecasts for Australian Herring. 2. Transition Australian Herring from bait to the higher-value human consumption market. 3. Development of three value-add Australian Herring products. 4. Identification of methods of full utilisation of Australian Herring waste products. 5. Development of effective market strategies to introduce value-add Australian Herring products to the retail market. Read moreRead less
Bringing The Iconic Australian Herring (Arripis Georgianus) To The Food Service And Retail Market – Phase Two
Funder
Fisheries Research and Development Corporation
Funding Amount
$169,000.00
Summary
The WA commercial herring fishery recently reopened following improvements in the stocks sustainability assessments. The product has traditionally been predominantly used for bait. This project, in partnership with herring producers, processors and retailers, will commence with a historical and current status review and consultation to better understand barriers and opportunities for commercial success of herring products for human consumption. Review of the commercial success or otherwise of ....The WA commercial herring fishery recently reopened following improvements in the stocks sustainability assessments. The product has traditionally been predominantly used for bait. This project, in partnership with herring producers, processors and retailers, will commence with a historical and current status review and consultation to better understand barriers and opportunities for commercial success of herring products for human consumption. Review of the commercial success or otherwise of similar underutilised species (such as Australian Salmon) will also be included. From this review, it is intended to identify, develop and implement three new retail and/or food service opportunities for herring for human consumption. Such opportunities, informed by the review, may be new product based (incorporating alternate processing strategies and/or 100% utilisation principles) or focussed on new marketing strategies. Evaluation for future commercial success will be economic, logistical and technical and will use evaluation metrics developed in previous projects. An enhanced use of herring for human consumption may not only increase profitability but may also lead to greater stock access for fishers. A framework for improving commercial success of such underutilised species research projects(reported in FRDC 2017/185) may be further extended by the study. Objectives: 1. Identify options to value add and (where possible) fully utilise the Australia Herring through the human consumption market 2. Investigate, implement and evaluate up to three human consumption market opportunities for Australian Herring-based products 3. Document and extend the developed supply chain framework methodology to get proposed new products to the market and explain how it can be replicable for other similar underutilised / lesser-known species Read moreRead less
Researching, Trialling And Evaluating A Market Driven Approach To Commercialising A Range Extended Marine Species - Tasmanian Wild Sea Urchin (Longspined Sea Urchin)
Funder
Fisheries Research and Development Corporation
Funding Amount
$560,000.00
Summary
Commercial in confidence. To know more about this project please contact FRDC. Objectives: Commercial in confidence
Investigation And Improvement Of Live Blue Swimmer Crab Handling In NSW
Funder
Fisheries Research and Development Corporation
Funding Amount
$102,107.00
Summary
As the NSW fishing industry moves forward into the future with quota managed fisheries, there is a need for industry to develop procedures and process on catching, holding and transporting Blue swimmer crab that would value add to the wild harvest sector’s product – particularly for the live sales market.
The current market is predominantly made of sales of cooked and raw blue swimmer crabs. An approx. price range of blue swimmer crab for 2015 / 2016 was $8.50 < $9.00 per kilo. The liv ....As the NSW fishing industry moves forward into the future with quota managed fisheries, there is a need for industry to develop procedures and process on catching, holding and transporting Blue swimmer crab that would value add to the wild harvest sector’s product – particularly for the live sales market.
The current market is predominantly made of sales of cooked and raw blue swimmer crabs. An approx. price range of blue swimmer crab for 2015 / 2016 was $8.50 < $9.00 per kilo. The live trade in blue swimmer crab in 2016 / 2017 is approx. $20.00 per kilo. A move to selling into the live market would provide a better return for effort and would help in maximizing return on investment in the blue swimmer crab quota fishery.
The “Live Blue Swimmer Crab” trade is in its infancy and it is timely to invest in technologies that will assist in lowering the mortality rates of these animals. Any investment now will accelerate the development of this fishery and ensure the best chance for the restructure of the NSW fishery to achieve its goals.ie viability and efficient use of a quota species.
The industry needs to have an easy to read handling guideline developed and training workshops to improve their access to the market and reduce mortality rates.
Objectives: 1. To produce handling guidelines and conduct a series of industry training workshops to reduce the mortality rate of blue swimmer crabs and thereby increase the volume of live product to market 2. To improve fishermen returns who adopt the guidelines and undertake the training provided Read moreRead less
Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying c ....Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying cutting edge genome biology tools and algorithms. The economically significant study system is the devastating wheat stripe rust fungus. This pathogen costs Australian farmers over $100 million a year. New understanding is expected to lead to better disease management, reduced fungicide applications, and increased yields.Read moreRead less
Diagnostic Detection Of Aquatic Pathogens Using Real-time Next Generation Sequencing
Funder
Fisheries Research and Development Corporation
Funding Amount
$216,000.00
Summary
Current diagnostic programs generally rely on highly -specific assays for pathogen detection. While these techniques are invaluable, they are one dimensional and do not provide detailed information critical to a disease investigation. These gaps include the inability to detect unknown pathogens and potential variants of know pathogens and provide no additional genomic or transcriptomic data. Moreover, samples must be shipped to trained personnel in a laboratory, further delaying the time to diag ....Current diagnostic programs generally rely on highly -specific assays for pathogen detection. While these techniques are invaluable, they are one dimensional and do not provide detailed information critical to a disease investigation. These gaps include the inability to detect unknown pathogens and potential variants of know pathogens and provide no additional genomic or transcriptomic data. Moreover, samples must be shipped to trained personnel in a laboratory, further delaying the time to diagnosis. The MinION, on the other hand, can theoretically detect any pathogen and can potentially be deployed to the field. Moreover, the MinION can rapidly generate full-length genomes, allowing for epidemiological tracking of viral or bacterial strains in near real-time. Such rapid data, which cannot be obtained as quickly using existing methods, are vital if the intention is to intervene in an outbreak and reduce impacts on the productivity and profitability of aquaculture facilities. For example, a rapid, early diagnosis may allow mitigating actions to be taken on-farm, such as the diversion of intake water, movement restrictions of stock and the isolation of infected ponds. These qualities make the MinION an attractive complimentary platform to fill several gaps in the data obtained during disease outbreak investigations, or routine diagnostics, and potentially for use in the field. However, results from the misuse or lack of understanding of the technology could also have adverse regulatory implications for aquaculture industries. For example, without appropriate guidelines, an inexperienced diagnostician may misinterpret a distant DNA match in a pathogen database as a significant result, this may create unwanted attention to industry and potential stock destruction or changes to disease status that are unjustified. Thus, it is critical that the MinION is evaluated at the Australian Animal Health Laboratory, and guidelines and procedures are developed for accurate diagnostic evaluations. The activities detailed in this application will establish the feasibility of using the MinION for diagnostic applications, and ensure that the data is reliably generated and interpreted appropriately.
Objectives: 1. Evaluate if MinION data meets or exceeds the data obtained using established laboratory-based NGS platforms. Objectives (1) and (2) align with Methods section (1).The first objective of this project is to demonstrate if the MinION can obtain quality genome assemblies of known pathogens, such as WSSV, AHPND, OsHV-1 and HaHV that have been created using existing NGS technology. Moreover, determine if the MinION is capable of producing a diagnostic result more rapidly and with greater confidence than traditional techniques. STOP/GO POINT: If MinION data does not produce reliable genome assemblies, no improvement in genome quality, or is significantly more laborious to set-up/run or analyse than existing NGS technologies, do not proceed with objective 2. 2. Evaluate the performance of the MinION using existing diagnostic extraction techniques and produce robust methods and protocols for sample preparation, sequencing and data analysis. This objective will optimise MinION protocols for sample pre-processing, optimal sequencing conditions, and data post-processing. We will then evaluate the MinION data produced from a range of aquatic organisms against data produced using traditional techniques from the same samples. STOP/GO POINT: If after these optimisations, the MinION cannot detect pathogens as reliably as traditional techniques, do not proceed with objective 3. 3. Compare the applicability of MinION to standard molecular assays for identification of pathogens in diagnostic samples. Objective (3) is aligned with Methods section (2).In this objective, diagnostic samples will be tested using existing diagnostics tools (qPCR, cPCR) and MinION sequencing. Analysis between the methods will be detailed, including time to result, pathogen identity and genomic information. This objective will not only provide an insight into real-time sequencing for diagnostics, but in addition the feasibility of MinION technology for field application in the future. Read moreRead less
Aquatic Animal Health And Biosecurity Subprogram: Comparative Pathogenicity Of Exotic Acute Hepatopancreatic Necrosis Disease (AHPND) And The Presumptive Bacterial Hepatopancreatitis Detected In Farmed Penaeus Monodon In Queensland
Funder
Fisheries Research and Development Corporation
Funding Amount
$131,106.00
Summary
Australian prawn production, forecast at 24 kilotonnes in 2014/15, is valued at >$310 million. The prawn fishery is an important natural resource that supports a substantial export industry. Prawn aquaculture in northern Australia accounts for approximately 20% of the total volume of Australian production. The new, emerging disease syndrome, characterised by hepatopancreatitis and mortalities in farmed P monodon, was first reported in north Queensland in early 2015. The disease was again detecte ....Australian prawn production, forecast at 24 kilotonnes in 2014/15, is valued at >$310 million. The prawn fishery is an important natural resource that supports a substantial export industry. Prawn aquaculture in northern Australia accounts for approximately 20% of the total volume of Australian production. The new, emerging disease syndrome, characterised by hepatopancreatitis and mortalities in farmed P monodon, was first reported in north Queensland in early 2015. The disease was again detected in late 2015 and emerged in central Queensland in early 2016. The disease in two prawn farming regions in Queensland is ongoing. While there are similarities with the emerging disease in central and north Queensland with exotic AHPND, the following important information is still unknown:
1) what is the variability (if any) in host bacterial strains associated with the AHPND toxin genes in diseased prawns in Queensland, particularly between the two different regions currently affected?
2) what is the pathogenicity of Australian bacterial isolates containing the AHPND toxin genes to P. monodon and P merguiensis how does this compare to disease caused by exotic AHPND isolates?
3) the preliminary WGS analysis needs to be repeated/confirmed using a more stringent and advanced platform.
This project will characterise the causative agent(s) and hepatopancreatitis disease in Australian farmed P. monodon. This information is critical for the prawn industry, policy-makers and regulators in order to respond to the disease. The Project aligns with Key Research Area 6.2.1 of the FRDC AAHS R&D Plan “Knowledge about new and emerging infectious diseases”.
Objectives: 1. Compare the pathogenicity of exotic AHPND and the presumptive bacterial hepatopancreatitis in Penaeus monodon and P. merguensis. 2. Compare the pathology caused by exotic AHPND and the presumptive bacterial hepatopancreatitis in Penaeus monodon and P. merguensis. 3. Determine the whole genome sequence of the Vibrio harveyi strain from farmed Penaeus monodon and P. merguensis presumptive bacterial hepatopancreatitis. 4. Optimise, evaluate through inter-laboratory testing and then implement improved diagnostic tests for the Pir toxin gene. Read moreRead less