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…

Water is the most abundant active compound in wine!

Proton relaxation in model and real wines was investigated by fast field cycling NMR relaxometry. Albeit protons of wine are largely belonging to water molecules, their magnetic relaxation rates actually depend on various physico-chemical parameters related to the state of the wine and to its composition.

Uve e vini in vulcaniti basiche anorogeniche dei lessini meridionali, impronta petrochimica e assimilazione di metalli pesanti

Nel 2009 sono stati prelevati e analizzati mediante XRF (X-ray fluorescence) campioni di suolo, in vigneti sperimentali siti nelle province di Vicenza e di Ancona. Sono stati inoltre determinati in 2 campioni di mosto e 2 di vino delle varietà Verdicchio e Refosco dal peduncolo rosso, ed in 2 di uva Refosco dal peduncolo rosso, gli elementi in traccia mediante ICP-MS (Inductively coupled plasma-mass spectrometry).

Grapevine sugar concentration model in the Douro Superior, Portugal

Increasingly warm and dry climate conditions are challenging the viticulture and winemaking sector. Digital technologies and crop modelling bear the promise to provide practical answers to those challenges. As viticultural activities strongly depend on harvest date, its early prediction is particularly important, since the success of winemaking practices largely depends upon this key event, which should be based on an accurate and advanced plan of the annual cycle. Herein, we demonstrate the creation of modelling tools to assess grape ripeness, through sugar concentration monitoring. The study area, the Portuguese Côa valley wine region, represents an important terroir in the “Douro Superior” subregion. Two varieties (cv. Touriga Nacional and Touriga Franca) grown in five locations across the Côa Region were considered. Sugar accumulation in grapes, with concentrations between 170 and 230 g l-1, was used from 2014 to 2020 as an indicator of technological maturity conditioned by meteorological factors. The climatic time series were retrieved from the EU Copernicus Service, while sugar data were collected by a non-profit organization, ADVID, and by Sogrape, a leading wine company. The software for calibrating and validating this model framework was the Phenology Modeling Platform (PMP), version 5.5, using Sigmoid and growing degree-day (GDD) models for predictions. The performance was assessed through two metrics: Roots Mean Square Error (RMSE) and efficiency coefficient (EFF), while validation was undertaken using leave-one-out cross-validation. Our findings demonstrate that sugar content is mainly dependent on temperature and air humidity. The models achieved a performance of 0.65

Dissecting the polysaccharide‐rich grape cell wall matrix during the red winemaking process, using high‐throughput and fractionation methods

Limited information is available on grape wall-derived polymeric structure/composition and how this changes during fermentation. Commercial winemaking operations use enzymes that target the polysaccharide-rich polymers of the cell walls of grape tissues to clarify musts and extract pigments during the fermentations. In this study we have assessed changes in polysaccharide composition/ turnover throughout the winemaking process by applying recently developed cell wall profiling approaches to both wine and pomace polysaccharides. The methods included gas chromatography for monosaccharide composition (GC-MS), infra-red (IR) spectroscopy and comprehensive microarray polymer profiling
(CoMPP) using cell wall probes.

A worldwide perspective on viticultural zoning

Cet article répertorie les intérêts et problèmes du zonage viticole dans une perspective mondiale. Le zonage est un besoin pour chacun des vignobles mondiaux où il correspond à des applications, définitions et approches variées. Les objectifs du zonage changent de concert avec les besoins du marché mondial du vin, qui ne cesse de croître.