Philosophiae Doctor - PhD / South Africa (SA) is home to one of the six floral kingdoms of the world, and hosts a very diverse flora comprising an astonishing ~30,000 species. Herbal medicines play an important role in many of the diverse cultures of this country. Yet, agricultural production systems for most of these species are missing, and medicinal plants are usually collected in the wild. The endemic medicinal plants of SA produce a wide range of rare medicinally active compounds, which could be developed into drugs. Knowledge on the genes involved in the biosynthesis of these compounds could not only promote establishment of plant production systems, but also their biotechnological exploitation. Transcriptomics has been revolutionized by Next Generation Sequencing technologies, which can cost-efficiently provide a lot of information on plant genes and biosynthetic pathways.
This thesis focuses on the establishment of methodologies for high-throughput plant transcriptome research, including: 1) harvesting plant material suitable for high-quality RNA analysis from distant locations, 2) high-throughput, and inexpensive biochemical sample screening, 3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol rich plant material, and 4) biocomputational analysis of Illumina sequencing data, including quality control and pre-processing of data, de novo assembly of reads, protein prediction and functional transcriptome annotation. Rooibos (Aspalathus linearis) was chosen as the pilot plant, because it is one of the few indigenous SA medicinal plants that has been successfully cultivated as a commercial crop. It produces a wide range of phenolic compounds with health promoting properties (e.g. aspalathin and a phenylpropenoic acid glucoside with scientifically verified antidiabetic and cardioprotective effects). In the course of this study, seven rooibos transcriptomes were produced, assembled and functionally annotated, providing a first extensive dataset for identification of genes associated with economically important traits such as medicinal compound production, rooibos growth type characteristics and stress resistance.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:uwc/oai:etd.uwc.ac.za:11394/6921 |
| Date | January 2019 |
| Creators | Stander, Emily Amor |
| Contributors | Hesse, Uljana |
| Publisher | University of the Western Cape |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | English |
| Rights | University of the Western Cape |
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