School of Agriculture, Food and Ecosystem Sciences - Theses
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ItemTowards association studies in Pinus radiata D.Don - populations and wood property candidate-genes( 2006)In Australia and New Zealand Pinus radiata D. Don wood quality is receiving increasing interest from tree breeders. This is partly due to declining resource wood quality associated with more advanced generation breeds leading to increased rejection and product downgrading in processing. While log segregation and wood grading at mill-door yields immediate benefits to processors the underlying cause is not addressed. The only long-term solution is to include wood quality in breeding programs. Wood quality traits are costly and difficult to measure. Marker-assisted selection offers a potential solution and quantitative trait loci (QTL) mapping studies have been undertaken with the aim of facilitating this. It is becoming increasingly clear that in widely outcrossing species with long generation times and very large genomes these approaches will not work. The identification of the underlying genetic sites, or tightly linked marker sites, would rectify this and in model species linkage-map based cloning has been used extensively. This approach is also not practical in species such as P. radiata. Association testing combined with a candidate-gene approach is therefore widely believed to be one of the only methods remaining. This approach uses a priori information to select and then test the phenotypic effects of variants within candidate-gene loci. Implementation of these studies relies heavily on the results of other investigations, especially those that generate DNA sequence information. Also required is detailed knowledge of the genetic population structure, the patterns of nucleotide diversity and the patterns of linkage disequilibrium. On a more practical level suitable populations need to be identified while the current methods for the collection and handling of samples for molecular investigations are limiting. The selection of candidate genes is also a non-trivial process. For candidate-gene association studies to be successful in P. radiata all these factors need to be addressed. This formed the main aim of this thesis. A multi-pronged approach was used. Firstly, at the population level, the genetic resources available for association studies were identified and the underlying genetic population structure of these resources and the patterns of nucleotide diversity and linkage disequilibrium were investigated. Secondly, improved methods for the collection and isolation of genomic DNA were developed and thirdly, a small set of wood quality candidate-genes were selected and further characterised with the aim of identifying those with the most promise of harbouring causative variation for inclusion in future association studies. This was achieved by literature based review, linkage mapping onto wood property QTL maps and neutrality testing. Results include support for previous population genetic studies showing P. radiata to have a complex genetic structure compared to most pine species. This study also indicated significant levels of migration between the three mainland populations. Within the candidate-genes two, cinnamyl alcohol dehydrogenase and sucrose synthase, showed interesting patterns of population differentiation and/or nucleotide diversity while the results for one other gene, korrigan, did not agree with previous investigations.