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Towards breeding better oysters: a proteomic investigation of disease resistance in Sydney rock oysters
thesisposted on 2022-03-28, 12:28 authored by Vineet Vaibhav
Sydney Rock oysters (Saccostrea glomerata) are a native Australian oyster species present mainly along the eastern coast of New South Wales. These oysters are economically very important as they are consumed as food across Australia. Sydney Rock oysters are known in particular for their distinctive taste, making them one of the major aquaculture products of Australia. During the early 20th century, the introduction of modern farming methods resulted in rapid growth in Sydney Rock oyster production. However, during the 1970s production started to decline as a result of mass mortalities caused by different diseases such as Queensland Unknown (QX) and Winter Mortality (WM). These diseases, in addition to the changing environmental conditions such as water pollution, further diminished the production of oysters. While there has been some previous research on environmental and disease stress in oysters, the causes and impacts of different diseases on the Sydney Rock industry are relatively underexplored. This thesis makes an attempt to enhance our fundamental understanding of two diseases of Sydney Rock oysters - QX and WM - using quantitative shotgun proteomics. Winter mortality was previously believed to be caused by a protozoan - Bonamia roughleyi, however the exact aetiology is still not clear. Whereas, QX disease is known to be caused by a paramyxean protozoan, Marteilia sydneyi, and is the major cause of the mass mortality of Sydney Rock oysters. The current mode of mitigating the impact of diseases relies on the farming of selected line of Sydney Rock oysters. The selective breeding programme of Sydney Rock oysters was established by NSW DPI using the survivors of mass mortality as a pioneering parent population. However, this mode of selection lacked the biological information of selection mechanisms and therefore it is feared that inbreeding depression might affect the future generations. Therefore, for sustainable growth of the industry it is very important to understand the biological basis of selection. This thesis aims to understand the underlying molecular processes of better adaptability of selected lines of oysters against diseases, by identifying the proteomics differences in selected and unselected populations. Chapter 1 of this thesis deals with the proteomic investigation of oysters selected for WM. Using 2DE in association with LC-MS/MS, we identified differential proteomic expression of proteins involved in many different biological processes. The major focus of this thesis is on QX disease and the following three experimental chapters of the thesis addresses different aspects of QX disease of Sydney Rock oysters. Chapter 3 reports a time dependent proteomic response of Sydney Rock oyster populations. We have identified a pattern of cytoskeletal breakdown in this study which shows a stepwise breakdown of cytoskeletal proteins with the disease period progression. Chapter 4 investigated the differences and similarities between selected Sydney Rock oysters from the wild Sydney Rock oysters grown in the same estuary. This work showed that in spite of being grown very close to each other the proteomic differences between the two populations was significant, suggesting a lack of genetic exchange or cross breeding. Chapter 5 used digestive gut tissue of Sydney Rock oyster for studying the comparative proteomics using a cutting edge proteomic analysis technique known as SWATH-MS. For the peptide to spectrum matching we used a newly available, but still unannotated, genome sequence of Sydney Rock oysters, and we identified a much greater number of proteins as compared to previous studies using the Pacific oyster genome sequence as a reference. This study reiterates the importance of the availability of functionally annotated genome sequence information for proteomics studies. The findings of this study are the first step towards generation of an identified protein library of Sydney Rock oyster which will be highly valuable for future studies. Considered together, the body of work described in this thesis represents a significant advancement in our fundamental understanding of the molecular mechanisms and biology of disease resistance and progression in Sydney Rock oysters.