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…

Moderate wine consumption as part of a Mediterranean diet and lifestyle under debate

Moderate wine consumption – with the meals – represents one of the beneficial components of the traditional mediterranean diet (med diet) and a positive item in the med diet score [1,2, 3]. The med diet is considered one of the best diets in the world and the world health organisation (who) identified this eating pattern as an effective strategy to prevent non-communicable diseases (ncd), since it is associated with lower disease occurrence and all-cause mortality [4] . Numerous well-conducted epidemiological studies have also reported that light-to-moderate intake of wine/alcoholic beverages is not only related to a reduced risk of cardiovascular disease, but also to all-cause mortality.

The use of elicitors in the vineyard to mitigate the effects of climate change on wine quality

The wine sector is being directly affected by climate change. Temperatures above 30ºC can cause a lag between the ripening of the berry pulp (a rapid increase in sugar content) and the skin

TerraClim, an online spatial decision support system for the wine industry

Climate projections for the future suggest favourable conditions for some wine producing regions, but challenging conditions for others. For instance, temperature increases are likely to shift grapevine phenology, ripening and harvest dates, and potentially affect grape quality and yield.

“Garrigues”, part of the mediterranean vine terroirs

Les paysages viticoles méditerranéens présentent une originalité qui ne se retrouve nulle part ailleurs : ils associent des garrigues très odoriférantes à des parcelles de vignes souvent qualitatives. La connaissance empirique des vins du Languedoc par leurs dégustateurs a conduit la Chambre d’Agriculture de l’Hérault à supposer que les arômes de la garrigue environnante peuvent se retrouver dans les vins (arômes de ciste, de genévrier, … )

Effect of fungi addition, root preparation, and other factors on the success of vine replacement in an established vineyard

Dead or dying vines must be replaced regularly in order to ensure the sustainability of a vineyard. Successful plant replacement is crucial to maintain yield and quality by encouraging balanced root and leaf development in vines. However, young vines planted within an established vineyard encounter several problems, ranging from poor soil conditions to competition with older vines with well-established root systems.