terclim by ICS banner
IVES 9 IVES Conference Series 9 Activation of retrotransposition in grapevine

Activation of retrotransposition in grapevine

Abstract

Retrotransposons, particularly of the Ty-Copia and Ty-Gypsy superfamilies, represent the most abundant and widespread transposons in many plant genomes. Grapevine is no exception and it is clear that these mobile elements have played a major role in the evolution of Vitaceae genomes. While speculation abounds around the possible role of transposons in plant genomes, outside of the rather obvious involvement of retrotransposition in fueling genome expansion, there is little clarity of the actual role these elements have in both developing new genetic variation and in modulating epigenetic responses within genomes to changing climate. To this end we have been exploring de-novo assembled Sauvignon blanc and Pinot noir genomes with a view to catalogue retrotransposon loci to determine the structural intactness and thus age of insertion variation across a small number of clonal linages of these 2 varietals in an attempt to identify ‘live’ TE loci. Combining insights into insertional patterns with both short and long read transcriptome data has highlighted that only a small number of families and within these families and an even smaller number of discrete loci are responsible for ongoing retrotransposition. We are currently exploring means to alter the epigenomic landscape of grape genomes to allow heightened retrotransposon activity and thus mobilization. We will present how we are tracking this mobility using virus-like protein particle analysis (VLP-seq) to both identify families actively transposing and to study the genomic and epigenomic impact of this mobility prior to purifying selection.

DOI:

Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Article

Authors

Christopher Winefield1*, Suguru Sugiyama1,2, Haniyeh Shahab1,2, Annabel Whibley2, Darrell Lizamore2

1 Department of Wine Food and Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln university, New Zealand
2 Bragato Research Institute, Lincoln University, New Zealand

Contact the author*

Keywords

Grapevine, Transposon, Genomics, Epigenomics, Climate Adaptation

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

Crown procyanidin: a new procyanidin sub-family with unusual cyclic skeleton in wine

Condensed tannins (also called proanthocyanidins) are a widely distributed throughout in plants kingdom and are one of the most important classes of secondary metabolites, in addition, they are part of the human diet. In wine, they are extracted during the winemaking process from grape skins and seeds. These compounds play an important role in red wine organoleptic characteristics such as color, bitterness and astringency. Condensed tannins in red wine are oligomers and polymers of flavan-3-ols unit such as catechin, epicatechin, epigallocatechin and epicatechin-3-O-gallate. The monomeric units can be linked among them with direct interflavanoid linkage or mediated by aldehydes.

Overcoming habit formation in the production of wine

Evidence indicates that climate change affects the environment, human health, and well-being via drought, increasing greenhouse effect, and climatic catastrophes. As the wine sector is also negatively affected by climate change, the role of climate change mitigation and adaptation policies is important in wine production. One example of an adaptation policy is the implementation of grapevine genetics (duchene, 2016), while organic farming may be used as an approach to mitigate the consequences of climate change (vinci et al., 2022). To this end, the european commission’s objective is to reach the european green deal target of at least 25% of the european union’s agricultural land under organic farming by 2030.

Adsorption capacity of phenolics compounds by polyaniline materials in model solution

The aim of this work was to study the trapping capacity of four polyaniline polymers towards phenolic compounds in wine-like model solutions. METHODS: The model wine solution was composed of 12% (v/v) and 4 g/L of tartaric acid adjusted to pH = 3.6. A series of centrifuge tubes (15 mL) were filled with 10 mL of model solution enriched with 50 mg/L of five phenolic compounds (i.e., Gallic acid, caffeic acid, (+)-catechin, (-)-epicatechin, and rutin), and treated with different doses of PANI polymer (i.e., 0, 2, 4 and 8 g/L). After the addition of the polymer, the samples were stirred using a platform shaker at room temperature (20 ºC) for 2, 8, 16 and 24 h. All treatments included three replications.

Modeling from functioning of a grape berry to the whole plant

Grape quality is a complex trait that mainly refers to berry chemical composition, including sugars, organic acids, phenolics, aroma and aroma precursor compounds.

Untangling belowground response of grapevines to cover crop competition

Cover crops are planted in vineyards for multiple benefits including soil conservation, weed management, regulation of grapevine vegetative growth