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DDRAD-seq based identification of genetic markers to facilitate the assessment of clonal versus sexual reproduction in dichrostachys cinerea
Dichrostachys cinerea, commonly referred to as “sicklebush”, is a semideciduous nitrogen-fixing tree species belonging to the Fabaceae family and is native to parts of Africa, India and Northern Australia. In addition to propagation via seed dispersal, the species is capable of asexual reproduction...
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| Format: | Thesis |
| Language: | English Eng |
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Department of Molecular and Cell Biology
2025
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| _version_ | 1867613197304856576 |
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| access_status_str | Open Access |
| author | Lumley, Liam Lester |
| author2 | Ingle, Robert |
| author_browse | Ingle, Robert Lumley, Liam Lester |
| author_facet | Ingle, Robert Lumley, Liam Lester |
| author_sort | Lumley, Liam Lester |
| collection | Thesis |
| description | Dichrostachys cinerea, commonly referred to as “sicklebush”, is a semideciduous nitrogen-fixing tree species belonging to the Fabaceae family and is native to parts of Africa, India and Northern Australia. In addition to propagation via seed dispersal, the species is capable of asexual reproduction via the process of root suckering. D. cinerea can aggressively colonize grasslands and quickly becomes problematic given its ability to persist through treatments such as fire, chemical treatment and mechanical removal. Due to its shrub-like physiology; propensity for root suckering; and the production of large amounts of seed, removal efforts often fail, especially in areas where D. cinerea has established dense thickets. African savannahs in particular have experienced a rapid rise in woody plant encroachment, with D. cinerea often one of the major species held responsible, and it is a species of concern to local ecologists. While previous studies have investigated the various factors which contribute to woody plant encroachment within Savanna ecosystems, it is still unclear as to what role asexual reproduction plays in this phenomenon and current methods to study this are laborious and time consuming. This study sought to develop a genetic based workflow to allow the detection of clonal individuals in D. cinerea. To facilitate this study, 225 D. cinerea samples were collected across the species range of D. cinerea in South Africa. DNA extracted from these samples allowed for the identification 39 299 SNP markers generated from ddRAD-seq libraries. These SNPs were then used to elucidate the phylogenetic relationships between individuals in order to ascertain whether clonality could be detected within the species, via the use of a genetic-distance-based threshold value which would discriminate between clonal and non-clonal individuals. Findings from this study revealed that across its species range, D. cinerea consisted of a mixed cytotype population, exhibiting a clear phylogenetic divide between diploid and tetraploid individuals. Identity-by-state analysis of the Kruger National Park diploid population confirmed that naturally occurring clonal individuals could be detected via ddRAD-seq generated SNP markers. This workflow will facilitate the study of clonality in D. cinerea in future studies which seek to answer ecologically relevant questions. |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/42417 |
| institution | University of Cape Town (South Africa) |
| language | English Eng |
| last_indexed | 2026-06-10T12:32:18.917Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Department of Molecular and Cell Biology |
| publisherStr | Department of Molecular and Cell Biology |
| record_format | dspace |
| source_str | UCTD — University of Cape Town Open Access Repository |
| spelling | oai:open.uct.ac.za:11427/42417 DDRAD-seq based identification of genetic markers to facilitate the assessment of clonal versus sexual reproduction in dichrostachys cinerea Lumley, Liam Lester Ingle, Robert Lenhard, Michael cell biology Dichrostachys cinerea, commonly referred to as “sicklebush”, is a semideciduous nitrogen-fixing tree species belonging to the Fabaceae family and is native to parts of Africa, India and Northern Australia. In addition to propagation via seed dispersal, the species is capable of asexual reproduction via the process of root suckering. D. cinerea can aggressively colonize grasslands and quickly becomes problematic given its ability to persist through treatments such as fire, chemical treatment and mechanical removal. Due to its shrub-like physiology; propensity for root suckering; and the production of large amounts of seed, removal efforts often fail, especially in areas where D. cinerea has established dense thickets. African savannahs in particular have experienced a rapid rise in woody plant encroachment, with D. cinerea often one of the major species held responsible, and it is a species of concern to local ecologists. While previous studies have investigated the various factors which contribute to woody plant encroachment within Savanna ecosystems, it is still unclear as to what role asexual reproduction plays in this phenomenon and current methods to study this are laborious and time consuming. This study sought to develop a genetic based workflow to allow the detection of clonal individuals in D. cinerea. To facilitate this study, 225 D. cinerea samples were collected across the species range of D. cinerea in South Africa. DNA extracted from these samples allowed for the identification 39 299 SNP markers generated from ddRAD-seq libraries. These SNPs were then used to elucidate the phylogenetic relationships between individuals in order to ascertain whether clonality could be detected within the species, via the use of a genetic-distance-based threshold value which would discriminate between clonal and non-clonal individuals. Findings from this study revealed that across its species range, D. cinerea consisted of a mixed cytotype population, exhibiting a clear phylogenetic divide between diploid and tetraploid individuals. Identity-by-state analysis of the Kruger National Park diploid population confirmed that naturally occurring clonal individuals could be detected via ddRAD-seq generated SNP markers. This workflow will facilitate the study of clonality in D. cinerea in future studies which seek to answer ecologically relevant questions. 2025-12-09T11:43:47Z 2025-12-09T11:43:47Z 2025 2025-12-09T11:38:01Z Thesis / Dissertation Masters MSc http://hdl.handle.net/11427/42417 en Eng application/pdf Department of Molecular and Cell Biology Faculty of Science University of Cape Town |
| spellingShingle | cell biology Lumley, Liam Lester DDRAD-seq based identification of genetic markers to facilitate the assessment of clonal versus sexual reproduction in dichrostachys cinerea |
| thesis_degree_str | Master's |
| title | DDRAD-seq based identification of genetic markers to facilitate the assessment of clonal versus sexual reproduction in dichrostachys cinerea |
| title_full | DDRAD-seq based identification of genetic markers to facilitate the assessment of clonal versus sexual reproduction in dichrostachys cinerea |
| title_fullStr | DDRAD-seq based identification of genetic markers to facilitate the assessment of clonal versus sexual reproduction in dichrostachys cinerea |
| title_full_unstemmed | DDRAD-seq based identification of genetic markers to facilitate the assessment of clonal versus sexual reproduction in dichrostachys cinerea |
| title_short | DDRAD-seq based identification of genetic markers to facilitate the assessment of clonal versus sexual reproduction in dichrostachys cinerea |
| title_sort | ddrad seq based identification of genetic markers to facilitate the assessment of clonal versus sexual reproduction in dichrostachys cinerea |
| topic | cell biology |
| url | http://hdl.handle.net/11427/42417 |
| work_keys_str_mv | AT lumleyliamlester ddradseqbasedidentificationofgeneticmarkerstofacilitatetheassessmentofclonalversussexualreproductionindichrostachyscinerea |