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Transcriptional regulation of seasonal desiccation tolerance in the fronds and rhizome of the fern Anemia caffrorum
Agriculture in drought-prone regions of the world is at increasing risk as climate change causes more intense and extended droughts. Desiccation tolerant plants are capable of surviving long periods of severe water loss (> 95% of cellular water) and are therefore prominent models for the production...
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| Format: | Thesis |
| Language: | English |
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Department of Molecular and Cell Biology
2024
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| _version_ | 1867613284006363136 |
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| access_status_str | Open Access |
| author | Khan, Farrah |
| author2 | Farrant, Jill Margaret |
| author_browse | Farrant, Jill Margaret Khan, Farrah |
| author_facet | Farrant, Jill Margaret Khan, Farrah |
| author_sort | Khan, Farrah |
| collection | Thesis |
| description | Agriculture in drought-prone regions of the world is at increasing risk as climate change causes more intense and extended droughts. Desiccation tolerant plants are capable of surviving long periods of severe water loss (> 95% of cellular water) and are therefore prominent models for the production of climate smart crops. The fern Anemia caffrorum is a particularly interesting model as it is capable of seasonal desiccation tolerance. In winter, when water availability is high, desiccation sensitive (DS) fronds are produced by the rhizome. In summer, when water availability is low, desiccation tolerant (DT) fronds are produced. Seasonal desiccation tolerance conferred to crops would allow for the maximization of food yields when water is available and prioritization towards survival when water is scarce. In this study transcriptional regulation of A. caffrorum desiccation tolerance in the fronds and rhizomes was explored. In particular, rhizomes were of interest as they have been postulated as the regulator of frond phenotype (DS/DT). Fronds and rhizomes were subjected to desiccation and tissues of different water contents were collected. Tissue from the fronds of both phenotypes (DS/DT) at full turgor (approximately 100% RWC), 55% RWC, 30% RWC, 10% RWC and 24-hours post rehydration were chosen. Tissue from the rhizomes producing DS fronds (winter rhizomes) and those producing DT fronds (summer rhizomes) was collected at 100% RWC and 30% RWC. Methods for isolating total RNA from all tissue types, of sufficient purity and yield, for next generation sequencing (NGS) experimentation were established. These samples were used to conduct short- and long-read sequencing for transcriptome assembly and gene expression studies. Transcriptome assembly using long read data outperformed de novo short read assembly as it resulted in greater rates of annotation and yielded a less fragmented assembly. The transcriptome was determined to be of a high-quality and was used to perform differential expression (DE) studies. DE studies showed that DS fronds had initiated senescent processes by 55% RWC which was only realised after rehydration. DT fronds were able to survive a desiccation event through several constitutive and inducible effects that were more reminiscent of desiccation tolerance in angiosperms than that of bryophytes. However, a relatively low transcriptional response compared to angiosperm desiccation tolerant plants, was a feature of bryophytic-type desiccation tolerance. Therefore A. caffrorum, like other ferns, demonstrated a mixed model of desiccation tolerance. DE studies of the rhizome provided several insights into canonical mechanisms of desiccation tolerance of the underground organ, alternate seasonal strategies, the role of the organ in frond phenotype regulation and cross-organ dynamics. Firstly, at 30% RWC rhizomes were postulated to be fully prepared for desiccation 3 and achieved this status through many common features observed in angiosperm resurrection plants. The strong presence of chloroplastic protective proteins in this response highlighted the likely transport of such transcripts to newly emerging fronds. In the reverse direction, rhizomes appeared to acquire sucrose and transcripts required for the recruitment of endophytic fungi from the fronds. Finally, severely dehydrated rhizomes showed prominent upregulation of genes that are responsible for leaf senescence, leaf development and initiation of spore production which was highly correlated with ABA-regulation. Also, under the control of ABA, was the production of transcripts that ultimately initiate the production of orange, trichomelike scales which are a key feature of the DT phenotype. Not under the control of ABA regulation, but relevant to the DT phenotype, were genes that promote dwarfism and reduced photosynthetic potential in fronds. Altogether, the study has provided possible candidate genes that may govern the DT phenotype and has underscored the significant interplay between these organs in achieving seasonal tolerance. |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/39576 |
| institution | University of Cape Town (South Africa) |
| language | eng |
| last_indexed | 2026-06-10T12:33:41.762Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| 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:11427/39576 Transcriptional regulation of seasonal desiccation tolerance in the fronds and rhizome of the fern Anemia caffrorum Khan, Farrah Farrant, Jill Margaret Rafudeen Mohamed Molecular and Cell Biology Agriculture in drought-prone regions of the world is at increasing risk as climate change causes more intense and extended droughts. Desiccation tolerant plants are capable of surviving long periods of severe water loss (> 95% of cellular water) and are therefore prominent models for the production of climate smart crops. The fern Anemia caffrorum is a particularly interesting model as it is capable of seasonal desiccation tolerance. In winter, when water availability is high, desiccation sensitive (DS) fronds are produced by the rhizome. In summer, when water availability is low, desiccation tolerant (DT) fronds are produced. Seasonal desiccation tolerance conferred to crops would allow for the maximization of food yields when water is available and prioritization towards survival when water is scarce. In this study transcriptional regulation of A. caffrorum desiccation tolerance in the fronds and rhizomes was explored. In particular, rhizomes were of interest as they have been postulated as the regulator of frond phenotype (DS/DT). Fronds and rhizomes were subjected to desiccation and tissues of different water contents were collected. Tissue from the fronds of both phenotypes (DS/DT) at full turgor (approximately 100% RWC), 55% RWC, 30% RWC, 10% RWC and 24-hours post rehydration were chosen. Tissue from the rhizomes producing DS fronds (winter rhizomes) and those producing DT fronds (summer rhizomes) was collected at 100% RWC and 30% RWC. Methods for isolating total RNA from all tissue types, of sufficient purity and yield, for next generation sequencing (NGS) experimentation were established. These samples were used to conduct short- and long-read sequencing for transcriptome assembly and gene expression studies. Transcriptome assembly using long read data outperformed de novo short read assembly as it resulted in greater rates of annotation and yielded a less fragmented assembly. The transcriptome was determined to be of a high-quality and was used to perform differential expression (DE) studies. DE studies showed that DS fronds had initiated senescent processes by 55% RWC which was only realised after rehydration. DT fronds were able to survive a desiccation event through several constitutive and inducible effects that were more reminiscent of desiccation tolerance in angiosperms than that of bryophytes. However, a relatively low transcriptional response compared to angiosperm desiccation tolerant plants, was a feature of bryophytic-type desiccation tolerance. Therefore A. caffrorum, like other ferns, demonstrated a mixed model of desiccation tolerance. DE studies of the rhizome provided several insights into canonical mechanisms of desiccation tolerance of the underground organ, alternate seasonal strategies, the role of the organ in frond phenotype regulation and cross-organ dynamics. Firstly, at 30% RWC rhizomes were postulated to be fully prepared for desiccation 3 and achieved this status through many common features observed in angiosperm resurrection plants. The strong presence of chloroplastic protective proteins in this response highlighted the likely transport of such transcripts to newly emerging fronds. In the reverse direction, rhizomes appeared to acquire sucrose and transcripts required for the recruitment of endophytic fungi from the fronds. Finally, severely dehydrated rhizomes showed prominent upregulation of genes that are responsible for leaf senescence, leaf development and initiation of spore production which was highly correlated with ABA-regulation. Also, under the control of ABA, was the production of transcripts that ultimately initiate the production of orange, trichomelike scales which are a key feature of the DT phenotype. Not under the control of ABA regulation, but relevant to the DT phenotype, were genes that promote dwarfism and reduced photosynthetic potential in fronds. Altogether, the study has provided possible candidate genes that may govern the DT phenotype and has underscored the significant interplay between these organs in achieving seasonal tolerance. 2024-05-06T13:53:19Z 2024-05-06T13:53:19Z 2023 2024-05-06T13:49:45Z Thesis / Dissertation Doctoral PhD http://hdl.handle.net/11427/39576 eng application/pdf Department of Molecular and Cell Biology Faculty of Science |
| spellingShingle | Molecular and Cell Biology Khan, Farrah Transcriptional regulation of seasonal desiccation tolerance in the fronds and rhizome of the fern Anemia caffrorum |
| thesis_degree_str | Doctoral |
| title | Transcriptional regulation of seasonal desiccation tolerance in the fronds and rhizome of the fern Anemia caffrorum |
| title_full | Transcriptional regulation of seasonal desiccation tolerance in the fronds and rhizome of the fern Anemia caffrorum |
| title_fullStr | Transcriptional regulation of seasonal desiccation tolerance in the fronds and rhizome of the fern Anemia caffrorum |
| title_full_unstemmed | Transcriptional regulation of seasonal desiccation tolerance in the fronds and rhizome of the fern Anemia caffrorum |
| title_short | Transcriptional regulation of seasonal desiccation tolerance in the fronds and rhizome of the fern Anemia caffrorum |
| title_sort | transcriptional regulation of seasonal desiccation tolerance in the fronds and rhizome of the fern anemia caffrorum |
| topic | Molecular and Cell Biology |
| url | http://hdl.handle.net/11427/39576 |
| work_keys_str_mv | AT khanfarrah transcriptionalregulationofseasonaldesiccationtoleranceinthefrondsandrhizomeofthefernanemiacaffrorum |