Doctoral Degrees (Genetics)

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Browsing Doctoral Degrees (Genetics) by Author "Coetzee, Beatrix"

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    Genome and transcriptome sequencing of vitis vinifera cv pinotage
    (Stellenbosch : Stellenbosch University, 2018-03) Coetzee, Beatrix; Burger, Johan T.; Maree, H. J.; Stellenbosch University. Faculty of AgriScience. Dept. of Genetics.
    ENGLISH ABSTRACT: Examining the genetic basis of natural phenotypic variation, and the transfer of this knowledge to a breeding program for improved crop cultivars or livestock races, is a major goal for biological sciences. As grapevine (Vitis vinifera) is one of the most important crop plants in the world, research into its genetics is imperatave, both in terms of sustainable food production and the vast economic impact of the wine industry. Grapevine displays a great level of intraspecies phenotypic diversity in viticultural and oenological traits, between cultivars. Understanding this genetic diversity is an important step towards developing improved grapevine cultivars, but also the conservation of the important traditional cultivars. Vitis vinifera cv Pinotage is an artificial Pinot noir/ Cinsaut cross, created with the South African climate and growing conditions in mind. Today it is a commercial cultivar, used for the production of premium wines, deeply rooted in the South African wine culture and history. This study focused on the next-generation sequencing and bioinformatic analysis of the Pinotage genome and transcriptome. A de novo assembly strategy was followed to produce the first Pinotage draft genome sequence. Sequencing read data were also aligned to the available reference Pinot noir genome, and from this alignment the Pinotage/ Pinot noir variant density, determined. This was followed by a more in-depth focus on a number of functional gene clusters with more than 50% of their genes influenced by these variants. Furthermore, this is the first research to lend scientific support to the current wine trend of exclusive, superior wines produced from old vineyards. These old-vine wines are assumed to have a deeper character and more flavour. To explore the role of genetics and differential gene expression in this phenomenon, RNA-seq data were used to survey and compare the leaf and berry transcriptomes of young and old Pinotage vines, at harvest. Differential gene expression between young and old vines was studied, and the involvement of these genes in fruit ripening, discussed. A general trend towards delayed ripening in older vines was observed. This suggests that the berries remain attached to the vine for a longer period, thereby allowing more time for flavour compounds to accumulate. In the final part of the study, the Pinotage genome and transcriptome data were combined to identify Pinotage genes present in neither the reference Pinot noir PN40024 nor ENTAV115. These genes were classified as both structural and regulatory genes and it was shown that genes involved in the stress response network are a major gene class contributing to the genetic differences between Pinotage and Pinot noir. A plant species is constantly challenged by various biotic and abiotic stresses and it is an evolutionary investment to diversify genes responsible for stress response, to be able to efficiently overcome these stresses. The information generated in this study will aid in grapevine breeding programs for sustainable production of high quality wine in a changing environment.