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…

Characterization of the thiol aromatic potential of a new resistant grape variety: Floreal

Aims: Due to climate change and the desire to decrease enological inputs (organic farming), the vineyard has to be modified and the selection of new resistant grape varieties as an alternative is researched intensively today. From January 2018, four new grape varieties that are resistant against mildew and odium have been added to the official

Targeted and untargeted 1H-NMR analysis for sparkling wine’s authenticity

Studies on wineomics (wine’s metabolome) have increased considerably over the last two decades. Wine results from many environmental, human and biological factors leading to a specific metabolome for each terroir. NMR metabolomics is a particularly effective tool for studying the metabolome since it allows the rapid and simultaneous detection of major compounds from several chemical families.1 Quantitative NMR has already proven its effectiveness in monitoring the authenticity of still wines.

Comparing the chemical and sensory consequences of grapevine smoke exposure in grapes and wine from different cultivars and different wine regions in Australia

Aim: This study aimed to benchmark the chemical and sensory consequences of grapevine exposure to smoke, by comparing: (i) the concentration of volatile phenols and volatile phenol glycosides in control and smoke-affected grapes from different cultivars and different wine regions; and (ii) the chemical and sensory profiles of wines made from control and smoke-affected grapes, from different cultivars.  

Variety and climatic effects on quality scores in the Western US winegrowing regions

Wine quality is strongly linked to climate. Quality scores are often driven by climate variation across different winegrowing regions and years, but also influenced by other aspects of terroir, including variety. While recent work has looked at the relationship between quality scores and climate across many European regions, less work has examined New World winegrowing regions. Here we used scores from three major rating systems (Wine Advocate, Wine Enthusiast and Wine Spectator) combined with daily climate and phenology data to understand what drives variation across wine quality scores in major regions of the Western US, including regions in California, Oregon and Washington. We examined effects of variety, region, and in what phenological period climate was most predictive of quality. As in other studies, we found climate, based mainly on growing degree day (GDD) models, was generally associated with quality—with higher GDD associated with higher scores—but variety and region also had strong effects. Effects of region were generally stronger than variety. Certain varieties received the highest scores in only some areas, while other varieties (e.g., Merlot) generally scored lower across regions. Across phenological stages, GDD during budbreak was often most strongly associated with quality. Our results support other studies that warmer periods generally drive high quality wines, but highlight how much region and variety drive variation in scores outside of climate.

Landscape marketing and landscape reality: what is the relationship? The case of the Loire Valley vineyards

This issue poses two questions: the relationship between beauty and taste (is landscape quality an index of wine quality ?), and the gap or the conformity between our image of the “terroir” and the visible reality. The landscape is both an object and a representation.