Bush, David James
Eucalyptus cladocalyx is endemic to South Australia and has been planted extensively on farmland throughout southern Australia and in dry, Mediterranean climates overseas. Its wood is hard, strong and naturally durable, making it suitable for fuelwood and solid-wood applications. Domestication in Australia commenced in 2001, when 11 provenance-progeny trials were established. The breeding objective is to maximise sawlog production per hectare per year. This thesis, presented as six chapters,...[Show more] examines genetic aspects of these trials that will influence the future direction of the species' domestication program. Chapter 1 argues that traditional methods and assumptions historically used to identify selections in the first-generation breeding programs of the main commercial tree species can be improved upon in the following ways: (1) Examination of wood properties (in addition to growth and form traits) during the first generation, taking advantage of modern labour-saving techniques, rather than delaying until later generations when unidentified adverse genetic correlations between traits may be problematic. (2) Employing molecular markers to determine population genetic parameters and reconstruct pedigree and inbreeding information from families that have unknown or uncertain ancestry. (3) Using recently-developed mixed-modelling techniques that allow integration of marker-based pedigree and inbreeding information to model genotype-by-environment (GxE) interactions using large datasets. Chapter 2 examines genetic parameters including heritability of growth and wood natural durability traits and additive genetic correlations among traits. The use of near infrared reflectance as a low-cost method of screening durability traits such as decay mass loss and wood extractive content is also investigated. Chapter 3 examines the use of marker-based data to modify traditional assumptions made in analysis of first generation breeding populations. Previously published growth-trait estimates, together with an earlier isozyme study, indicated that the traditional approach may give upwardly biased heritability estimates due to high and heterogeneous selfing. Models were implemented that compared the approach of treating families as half-sibs with analyses based on previously existing isozyme estimates of heterogeneous family outcrossing to modify pedigree assumptions. The results of genotyping mature trees from the majority of families in the breeding population using single-nucleotide polymorphism (SNP) markers are presented in Chapter 4. Population structure and diversity, family relatedness, inbreeding and inbreeding depression were investigated. Chapter 5 integrates the marker-based estimates of family-level relatedness and inbreeding of Chapter 4 into a quantitative genetic analysis across sites using an extension of the methodology developed in Chapter 3. Individual-tree mixed models based on (i) the traditional half-sib family assumption and (ii) a modified mixed model incorporating marker-based data were compared. Analysis of GxE was performed across the 11 sites using individual-tree, factor analytic mixed models. Chapter 6 concludes that the prospects for genetic improvement of E. cladocalyx are good, due to ample, heritable genetic variation and absence of adverse genetic correlations among traits. Analyses with integrated molecular marker data were significantly improved, as traditional models were unsuitable due to the breeding population's heterogeneous and unusually high levels of inbreeding. Integration of marker data into first-generation analyses of eucalypt breeding populations is likely to find wider application in future.
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