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.

Download the abstract

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…

Exogeneous C-S lyase enzyme, a potential tool for thiol enhancement in wine or beer?

Varietal thiols are considered for years as key aroma compounds in many wines. Their main origin is the cleavage during alcoholic fermentation of S-conjugate precursors present in grapes and musts, even if the levels of precursors already identified struggle to completely explain the levels of thiols found in wine.

Read More

Preliminary results of the eliminary results of the characterizarion of Argentine wines and the foreseeing of the future effects of global warming on the quality and style

The few studies that relates the chemical composition and the organoleptic characteristics of Argentine wines with the origin show that climate is a very important factor.

Read More

Water resource management at high spatial resolution for sustainable adaptation to climate change in wine-growing terroirs

In the context of climate change, water availability, together with rising temperatures, is one of the main factors driving the relocation of viticulture to new regions.

Read More

Apoplastic pH influences Vitis vinifera Barbera recovery responses to short and prolonged drought 

Alteration of sap pH is one of the first chemical changes that occurs within the xylem vessels of plants exposed to drought. Xylem sap acidification accompanied by the accumulation of soluble sugars has been recently documented in several species (Sharp and Davis, 2009; Secchi and Zwieniecki, 2016). Here, Vitis vinifera plants of the anysohydric cultivar Barbera were exposed to either short (no irrigation; SD) or to prolonged drought (continual reduction of 10% water; PD). When comparable severe stress was reached, the potted grapes were re-watered. SD was characterized by fast (2–3 days) stomatal closure and high abscisic acid (ABA) accumulation in xylem sap (>400 μg L−1) and in leaf. In PD plants, the rise in ABA levels was considerably diminished.

Read More

Effect of mannoproteins extracted from Torulaspora delbrueckii on wine flavanol composition and on flavanol-salivary protein interactions

Global climate change is exerting an influence on vine phenology, leading to a decoupling of technological and phenolic maturity of grapes. This results in the modification of berry chemical composition, which can translate into wines with excessive astringency. The addition of mannoproteins (MP) to wine has been proposed as a way of mitigating this problem, since some studies have shown that MPs can modulate wine astringency. However, the mechanism underlying the astringency modulation effect of MPs is not well known and it seems to be dependent on the compositional and structural characteristics of the MP.

Read More