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…

Guard cells and stomatal movement reveal early molecular interaction between grapevine cells and esca-associated pathogens

Esca is one of the major grapevine trunk diseases that cause vineyards decline and important economic losses in vineyards.

The soil biodiversity as a support to environmental sustainability in vineyard

The environmental biodiversity is important to guarantee essential services to the living communities, its richness is a symptom of a minor disturbance and improves he environment biological quality.

Importance of matrix effects (wine composition) on protein stability tests of white and rosé wines

The presence of unstable proteins in wines can affect their stability and clarity. Before bottling, winemakers need to be sure that the wine is stable. A large number of stability tests have been proposed, usually based on heating a sample with a specific time-temperature couple. In practice, none is effective to accurately assess the risk of instability. Moreover, the interpretation of the results of these tests changes according to the region.

Comparison of various storage conditions to preserve polyphenols in red-grape pomace

Red grape pomace, a waste from wine production, can be valorised by extracting polyphenols, high-added value compounds used in cosmetics or oenology. For use at an industrial level, using green extraction techniques, pomace need to be stored before being processed. The aim of this study is to test various storage conditions in order to maintain high level of polyphenols over 180 days, while keeping storage cost economically interesting. In a first step, different storage conditions (ambient temperature or cooled (4°C) temperature, anaerobic (saturation with N2) or aerobic conditions, and addition of sulphur dioxide (SO2)) were compared on small samples (1 kg) packed in plastic pockets. The quality of storage was assessed by following the optical density of the pomace extract at 280 nm (DO 280 expressed as mg/l eq gallic acid), which is an indication of the amount of remaining extractable polyphenols.

FERMENTATION POTENTIAL OF INDIGENOUS NON-SACCHAROMYCES YEASTS ISOLATED FROM MARAŠTINA GRAPES OF CROATIAN VINEYARDS

The interest in indigenous non-Saccharomyces yeast for use in wine production has increased in recent years because they contribute to the complex character of the wine. The aim of this work was to investigate the fermentation products of ten indigenous strains selected from a collection of native yeasts established at the Institute for Adriatic Crops and Karst Reclamation in 2021, previously isolated from Croatian Maraština grapes, belonging to Hypopichia pseudoburtonii, Metschnikowia pulcherrima, Metschnikowia sinensis, Metschnikowia chrysoperlae, Lachancea thermotolerans, Pichia kluyveri, Hanseniaspora uvarum, Hanseniaspora guillermondii, Hanseniaspora pseudoguillermondii, and Starmerella apicola species, and compare it with commercial non-Saccharomyces and Saccharomyces strains.