The Pinotage genome: stress response genes are a major source of inter-cultivar genetic diversity

By Beatrix Coetzee

Grapevine cultivars display a great level of intra-species diversity in viticultural and oenological traits. Understanding this genetic diversity is an important step towards developing improved grapevine cultivars, but also for the conservation of the important traditional cultivars.

This study focused on the next-generation sequencing and bioinformatic analysis of the Pinotage genome and transcrip- tome. 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, and  deeply rooted in the South African wine culture and history.

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.

Pinotage genome and transcriptome data were also combined to identify Pinotage genes not present in the reference Pinot noir genome. These were classified as both structural and regulatory genes and it was shown that, especially genes involved in the stress response network, are a major gene class contributing to the genetic differences between Pinotage and Pinot noir. Since a plant species is constantly challenged by various biotic and abiotic stresses, it is an evolutionary investment to diversify genes involved in stress responses, to be able to efficiently overcome these stresses.

Researcher: Beatrix Coetzee

This project is funded by the Pinotage Association


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