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
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
Discovery Early Career Researcher Award - Grant ID: DE240100573
Funder
Australian Research Council
Funding Amount
$450,877.00
Summary
Genomics of extinction and isolation on Australian island arks. This project aims to measure the genetic health of key populations of threatened Australian mammals. With the highest rate of extinction in the world and over 30% of surviving species under immediate threat, Australian mammals require urgent focus to secure their future. This project focuses on island populations, which are increasingly used as sources to rewild mainland Australia. Using cutting-edge genomic tools, this project plan ....Genomics of extinction and isolation on Australian island arks. This project aims to measure the genetic health of key populations of threatened Australian mammals. With the highest rate of extinction in the world and over 30% of surviving species under immediate threat, Australian mammals require urgent focus to secure their future. This project focuses on island populations, which are increasingly used as sources to rewild mainland Australia. Using cutting-edge genomic tools, this project plans to determine the extent and nature of genetic variation, including harmful mutations, on islands and in declining mainland populations. The anticipated outcome is to understand how genetic factors contribute to extinction, to improve conservation strategies for threatened species.Read moreRead less
Early Career Industry Fellowships - Grant ID: IE230100048
Funder
Australian Research Council
Funding Amount
$466,097.00
Summary
Ammonium-selective membranes to shift water industry into circular economy. The project aims to develop ammonium-selective membranes which are urgently needed in Australian key industries for sustainable ammonia recovery. The project expects to construct the membranes to achieve desirable pore size and surface functionality for fast and selective ammonia transport. The developed membranes should make ammonia recovery from wastewater more effective and sustainable, leading to the healthy waterway ....Ammonium-selective membranes to shift water industry into circular economy. The project aims to develop ammonium-selective membranes which are urgently needed in Australian key industries for sustainable ammonia recovery. The project expects to construct the membranes to achieve desirable pore size and surface functionality for fast and selective ammonia transport. The developed membranes should make ammonia recovery from wastewater more effective and sustainable, leading to the healthy waterway and reduced energy for both ammonia production and removal. Recovered ammonia expects to produce valuable products, supporting agriculture industry and hydrogen economy. The developed membranes should enable water industry's shift into circular economy, providing significant economic and environmental benefits to Australia.Read moreRead less