Genome and transcriptome sequencing of vitis viniferacv pinotage

[摘要] ENGLISH ABSTRACT: Examining the genetic basis of natural phenotypic variation, and the transfer of this knowledgeto a breeding program for improved crop cultivars or livestock races, is a major goal forbiological sciences. As grapevine (Vitis vinifera) is one of the most important crop plants in theworld, research into its genetics is imperatave, both in terms of sustainable food productionand the vast economic impact of the wine industry. Grapevine displays a great level of intraspeciesphenotypic diversity in viticultural and oenological traits, between cultivars.Understanding this genetic diversity is an important step towards developing improvedgrapevine 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 Africanclimate and growing conditions in mind. Today it is a commercial cultivar, used for theproduction of premium wines, deeply rooted in the South African wine culture and history. Thisstudy focused on the next-generation sequencing and bioinformatic analysis of the Pinotagegenome and transcriptome.A de novo assembly strategy was followed to produce the first Pinotage draft genomesequence. Sequencing read data were also aligned to the available reference Pinot noirgenome, and from this alignment the Pinotage/ Pinot noir variant density, determined. Thiswas followed by a more in-depth focus on a number of functional gene clusters with more than50% of their genes influenced by these variants.Furthermore, this is the first research to lend scientific support to the current wine trend ofexclusive, superior wines produced from old vineyards. These old-vine wines are assumed tohave a deeper character and more flavour. To explore the role of genetics and differential geneexpression in this phenomenon, RNA-seq data were used to survey and compare the leaf andberry transcriptomes of young and old Pinotage vines, at harvest. Differential gene expressionbetween 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 suggeststhat the berries remain attached to the vine for a longer period, thereby allowing more time forflavour compounds to accumulate.In the final part of the study, the Pinotage genome and transcriptome data were combined toidentify 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 thatgenes involved in the stress response network are a major gene class contributing to thegenetic differences between Pinotage and Pinot noir. A plant species is constantly challengedby various biotic and abiotic stresses and it is an evolutionary investment to diversify genesresponsible for stress response, to be able to efficiently overcome these stresses. Theinformation generated in this study will aid in grapevine breeding programs for sustainableproduction of high quality wine in a changing environment.

[发布机构] Stellenbosch University