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.

The NSW oyster industry has suffered from QX disease and winter mortality for a very long time. It has responded to these disease challenges by vacating affected leases seasonally or in the case of Georges River by abondoning the infested part of the estuary. The history of inter-estuary transfer of oysters for on-growing has not allowed the development of resistant strains in NSW. However, if resistant strains of oysters are not developed, the industry will have no better management tool available in future than that used in the past, ie moving or selling oysters before a disease outbreak is expected or abondoning oyster leases.

If the opportunity for breeding QX disease resistance in Sydney rock oysters is not taken up, a unique opportunity will be lost, to use breeding lines previously selected for fast growth in the selection for disease resistance. It is important that breeding for QX resistance begins now, before another estuary is infested with this parasite. In Georges River, the industry responded to the QX outbreak by abandoning affected leases.

Growth rates in Sydney rock oysters have been improved by an average of 4% for the first generation of selection in Port Stephens. Now the initial progress has been made and four breeding lines are established, it is important that the momentum is maintained and selective breeding for fast growth is continued. The growth rate of the Port Stephens selection lines can be increased by 4% for each successive generation.

Growth rates in Sydney rock oysters can be improved by both selective breeding (an average of 4% faster growth for the first generation of selection) and triploidy (30-40% faster growth). However, triploids have not previously been produced from improved breeding lines. It is important to determine if improvements in growth rates by these two methods are additive. For example with triploids produced from improved breeding lines, a 30% increase in growth rate with triploidy plus another 8% for two generations of selective breeding may increase growth rates of oysters by 38%.