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…

Zoning of potential landscape and environment potential of the «Appellation d’Origine Contrôlée Costières de Nîmes»

The Union defence of the “appellation Costières de Nîmes” hired a reflection on the future of its territory production in the interests of preservation and enhancement.

DETERMINATION OF FREE AMINO ACIDS, AMINO ACID POTENTIAL AND PROTEASE ACTIVITY IN THE LEES AND STILL WINES OF CHAMPAGNE

Prior to winemaking, organic or mineral nitrogen compound concentrations are usually measured in the vineyard and in grape musts. These indicators facilitate vine cultivation decisions, usually through yield or vigor. During vinification, yeast and bacteria metabolize nitrogen compounds in the musts in order to generate biomass. After fermentation, the microorganisms rerelease a part of this nitrogen as soluble compounds into the wines. Another part remains bound in the lees and can be lost during racking. The must’s natural nitrogen quantities, additional supplements during fermentation, and lees contact management enhance the release of nitrogen compounds to the wines. During ageing these nitrogen compounds – primarily the amino acids – are implicated in the generation of odorous compounds such as heterocycles(1).

Characterization and application of silicon carbide (SiC) membranes to oenology

After fermentations, the crude wine is a turbid medium not accepted by the consumer therefore, it needs to be filtered

EFFECTS OF LEAF REMOVAL AT DIFFERENT BUNCHES PHENOLOGICAL STAGES ON FREE AND GLYCOCONJUGATE AROMAS OF SKINS AND PULPS OF TWO ITALIAN RED GRAPES

Canopy-management practices are applied in viticulture to improve berries composition and quality, having a great impact on primary and secondary grape metabolism. Among these techniques, cluster zone leaf removal (defoliation) is widely used to manage air circulation, temperature and light radiation of grape bunches and close environment. Since volatiles are quantitatively and qualitatively influenced by the degree of fruit ripeness, the level of solar exposure, and the thermal environment in which grapes ripen, leaf removal has been shown to affect volatile composition of grape berries [1].

Marketing terroir wines

The markets for quality wine are becoming more competitive as newer producers emerge and traditional producers improve their quality. The concept of terroir is one way to differenzi­ate wines in a competitive market and to enhance producer income.