Thesis
Unravelling the genetics of macadamia : integration of linkage and genome maps
Southern Cross University
Doctor of Philosophy (PhD), Southern Cross University
2020
DOI:
https://doi.org/10.25918/thesis.180
Metrics
27 File views/ downloads
180 Record Views
Abstract
The tree nut crop macadamia is cultivated from the subtropical Proteaceae species Macadamia integrifolia and M. tetraphylla that are endemic to eastern Australia. This thesis aimed to establish the first sequence-based genetic linkage maps for macadamia, with marker density suitable for genome anchoring.
Genetic linkage maps are linear representations of loci on chromosomes that reflect the distribution of recombination and other chromosomal scale attributes for a species. In order to develop accurate linkage maps for this poorly-studied outcrossing perennial, a deep understanding of the constraints affecting recombination and marker detection was required, followed by analysis of DNA markers to optimise information from progeny within a related set of segregating populations.
The thesis includes a literature survey of the existing genetic research that has been undertaken in macadamia, which is followed by an in depth investigation of factors affecting recombination. To develop genetic linkage maps with marker density suitable for genome anchoring four first generation populations were used to maximise the segregation patterns available within full-sib, biparental and self-pollinated progeny. DNA paternity analysis using SSR and SNP markers confirmed the parentage of 78% of the progeny in populations developed for this project, and also identified pollen contamination and self-fertilised progeny in each biparental controlled cross.
Stringent data filtering was implemented to identify reliable sequence based markers for mapping. Of the 16,136 markers identified, 4,266 overlapping subsets of sequence-tagged informative markers were available after filtering and used for subsequent mapping. Nine genetic linkage maps were produced, comprising 14 linkage groups, consistent with the karyotype for macadamia. Comparisons between individual maps indicated a high level of congruence, with minor discrepancies satisfactorily resolved within integrated maps. The production of integrated cultivar maps from multiple parental linkage maps increased marker density compared with component maps.
The use of multiple populations and maps, in combination, maximised the coverage of informative markers available and successfully anchored 70% of the M. integrifolia ‘741’ genome assembly. The maps, large number of sequence-based markers, and chromosome-scale genome assembly provides a toolkit to underpin future breeding and the long-term conservation of natural populations in eastern Australia. In particular, they will provide valuable resources for QTL mapping, genomic prediction and marker-assisted selection.
Details
- Title
- Unravelling the genetics of macadamia : integration of linkage and genome maps
- Creators
- Kirsty Simone Langdon
- Contributors
- Catherine Jane Nock (Supervisor) - Southern Cross UniversityGraham King (Supervisor) - Southern Cross University
- Awarding Institution
- Southern Cross University; Doctor of Philosophy (PhD)
- Theses
- Doctor of Philosophy (PhD), Southern Cross University
- Publisher
- Southern Cross University
- Number of pages
- xv, 199
- Identifiers
- 991012980198502368
- Copyright
- © KS Langdon 2020
- Academic Unit
- School of Environment, Science and Engineering; Southern Cross Plant Science
- Resource Type
- Thesis