Genomics of the Sydney rock oyster <i>Saccostrea glomerata</i> (Gould, 1850)

<p dir="ltr">Genetic variation can be managed for the long-term survival and performance of wild and farmed populations alike. Plentiful genetic variation enables adaptation to altered selection pressures such as changing environmental conditions, novel biotic interactions or disease outbreaks. Genetic variation can be exploited to improve the resilience of both farmed and natural populations. For the farming industry, this is driven by the motive of improving productivity. Potentially, some these very same traits desired by farmers would also benefit wild populations, such as resistance to known diseases and resilience to environmental stressors. However, given that future environmental challenges are difficult to predict, the selection of these traits should be balanced against a general objective of retaining genetic variation. </p><p dir="ltr">The Sydney rock oyster (<i>Saccostrea glomerata</i>) represents an interesting case highlighting the complementary nature of the conservation of wild populations and the improvement of aquaculture stock. Sydney rock oyster farming predominantly occurs within estuaries that support co-existing wild populations, meaning both groups face similar environmental and pathogenic pressures. As such, the goals of genetic improvement of wild and farmed populations are inextricably linked. Genetic gains in environmental resilience or disease resistance within wild or farmed populations could be harnessed and implemented within other populations, allowing selective breeding to help address both the rising desire to maintain and restore natural populations, and the need to increase food productivity to meet the demand of growing human populations. </p><p dir="ltr">In this thesis, I explore and compare the genetic resources that are available within wild and farmed Sydney rock oyster populations in eastern Australia, using thousands of genome-wide single nucleotide polymorphisms. The first data chapter (Chapter 2) elucidates the stock structure of wild Sydney rock oysters throughout the extent of their distribution on Australia’s east coast. A single genetic stock was identified, with a large effective population size and no evidence of a recent genetic bottleneck. Limited isolation by distance was detected. This was weakly associated with the strength of the east Australian current. Additional co-occurring <i>Saccostrea </i>specimens are noted within the northernmost region of the distribution. These are genetically identified in a subsection of the first data chapter. </p><p dir="ltr">Chapter 3 developed the first chromosome-level linkage map for <i>S. glomerata</i>. This resource was used to assess genome-wide genetic variation in the major aquaculture breeding lines. I determined that selective breeding of farmed Sydney rock oysters over many generations has not caused a significant loss of genetic variation within aquaculture stock. The two major breeding lines showed strong signs of genetic divergence from wild oysters, and from one another. Thirteen loci were found to be associated with this divergence, which may correspond to selection for disease resilience and fast growth. </p><p dir="ltr">In the third data chapter (Chapter 4), I used population branch statistics and a genome-wide association study to examine signals of selection associated with QX disease resilience in wild and selectively-bred oysters. QX disease is the main biotic factor that limits commercial Sydney rock oyster production in eastern Australia. For candidate loci, the relationship between allele frequencies and QX disease survival were examined within 27 family lines. Strong correlations were confirmed for 11 markers, with 7 of these located on a single chromosome. </p><p dir="ltr">In the final data chapter (Chapter 5), I examined heterozygosity-fitness correlations for two traits of interest for wild and farmed populations. The analysis showed that increased multilocus heterozygosity was correlated with QX disease survival. No significant relationship was found between multilocus heterozygosity and fast growth. This chapter also uncovered evidence for a biological trade-off between fast growth and QX disease survival. </p><p dir="ltr">Taken together, the genetic knowledge and resources presented in this thesis have the potential to facilitate a marker-assisted enhancement program for Sydney rock oysters, and assist in the genetic management of wild and farmed populations.</p>