terclim by ICS banner
IVES 9 IVES Conference Series 9 Using nanopore skim-sequencing to characterise regional epigenetic variability in New Zealand Sauvignon Blanc

Using nanopore skim-sequencing to characterise regional epigenetic variability in New Zealand Sauvignon Blanc

Abstract

Recent advancements in genomic sequencing technologies have enabled more detailed and direct studies of DNA methylation, which can help characterise epigenetic variations in plants. The Grapevine Improvement team at the Bragato Research Institute is studying the use of Oxford Nanopore sequencing to identify epigenetic changes associated with environmental differences among clonally-propagated grapevines.

This study involved sequencing DNA from the same Sauvignon Blanc clone, sourced from diverse New Zealand viticultural regions, using the PromethION platform. New base-calling models were used to characterise cytosine methylation in various contexts (CG, CHG, and CHH) alongside adenosine methylation. Subsampling revealed that low-depth skim sequencing (0.1x) is sufficient to distinguish genome-wide methylation profiles, with geographic location emerging as the predominant factor influencing epigenetic traits. The method of sample preservation, whether immediate snap-freezing or initial storage in desiccant, did not have a significant effect on the results.

 This research demonstrates the potential of low-depth nanopore sequencing for assessing epigenetic variability as influenced by environmental factors in plants. The approach holds promise for the investigation of the mechanisms that drive the expression of location-specific agronomic traits, forecasting climate-related epigenetic shifts, and facilitating the development of technologies aimed at inducing targeted epigenetic modifications.

DOI:

Publication date: June 13, 2024

Issue: Open GPB 2024

Type: Poster

Authors

Cen Liau1, Annabel Whibley1, Bhanupratap Vanga1, Solomon Wante1, Amy Hill1, Ellie Bradley1, Darrell Lizamore1*

1Grapevine Improvement Team, Bragato Research Institute, Lincoln, New Zealand

Contact the author*

Keywords

Nanopore sequencing, epigenetics, DNA methylation

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

Vine responses to two irrigation systems in the region of Vinhos Verdes

In this work we try to know the influence of two irrigation systems (Drip and Micro – jet ) with the same levels of water applied in an experimental vineyard in the region of Felgueiras.

Impact of changes in pruning practices on vine growth and yield

A gradual decline in vineyards has been observed over the past twenty years worldwide. This might be explained by the climate change, practices change or the increase of dieback diseases. To increase the longevity of vines, we studied the impact of different pruning strategies in four adult and four young vineyards located in France and Spain. In France, vineyards were planted with Cabernet franc on 3309C while Spanish trials were planted with Tempranillo grafted on 110R. Vegetative expression, yield, quality of berries and wood vessels conductivity were measured. The distribution of vegetative expression, yield and berry composition between primary and secondary vegetation were quantified. Finally, tomography was used to evaluate the implication of the treatments on sap flows.
First results show that i) the respectful pruning leads to an increase of 30 to 50% more secondary shoots than the aggressive pruning in France and between 15 and 20% in Spain, ii) there is no major effect on the yield over the first two years following the implementation of the new pruning practices, although the proportion of clusters from suckers is higher on the respectful pruning method. On young vines, the development of the trunk according to a respectful pruning leads to a loss of harvest 2 years after planting. This is due to the removal, on the future trunk, of the green suckers which carrying bunches. This operation carried out in spring rather than during winter pruning, would promote a better leaf / fruit balance when the plant comes into production, and could lead to better hydraulic conduction in the vessels of the trunk. Maintaining these trials for several years will provide more robust data to assess the impact of these practices on the vines over the long term.

A NEW STRATEGY AND METHODOLOGY FOR THE CHARACTERIZATION OF POLYPHENOLS IN FINING PRECIPITATE

Polyphenols are secondary metabolite widely distributed in plant kingdom such as in fruits, in grapes and in wine. During the winemaking process, polyphenols are extract from the skin and seed of the berries. Fining is an important winemaking step just before bottling which has an impact on wine stabilization and clarification. Most the time, fining agent are animal or vegetal protein while some of them can be synthetic polymer like PVPP or natural origin like bentonite.

Elicitors used as a tool to increase stilbenes in grapes and wines

The economic importance of grapevine as a crop plant makes Vitis vinífera a good model system to study the improvement of the nutraceutical properties of food products (Vezulli et al. 2007). Stilbenes in general, and trans-resveratrol in particular, have been reported to be responsible for various beneficial effects. Resveratrol´s biological properties include antibacteria and antifungal effects, as well as cardioprotective, neuroprotective and anticâncer actions (Guerrero et al. 2010 ). Stilbenes can be induced by biotic and abiotic elicitors since they are phytoalexins (Bavaresco et al. 2001).

Chemical and sensory diversity of regional Cabernet-Sauvignon wines

AIM: To investigate chemical and sensory drivers of regional typicity of Cabernet Sauvignon from different geographical regions of Australia.