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…

The limonene-derived mint aroma compounds in red wines. Recent advances on analytical, chemical aspects and sensory aspects

In recent years, the ageing bouquet of red Bordeaux wines has been partially unveiled by a chemical and sensory point of view1–3. Minty and fresh notes were found to play a key role in the definition of this complex concept, moreover the freshness dimension in fine aged red wines plays an important role in typicity judgement by wine professionals

Direct SPME GC-MS determination of volatile congeners in wines without sample pre-treatment

In this work “ethanol as an internal standard” method was used for the SPME GC-MS quantification of volatile congeners in wines. Our aim was to develop a fast and simple method of wine analysis without additional procedures, reagents etc. A row of standard solutions containing some frequently found congeners in wine was prepared gravimetrically. Suggested method was compared with traditional internal standard method.

Managing precision irrigation in vineyards: hydraulic and molecular signaling in eight grapevine varieties

Understanding the physiological and molecular bases of grapevine responses to mild to moderate water deficits is fundamental to optimize vineyard irrigation management and identify the most suitable varieties. In Mediterranean regions, the higher frequency of heat waves and droughts highlights the importance of precision irrigation to meet vine water demands and demonstrates the necessity for a deeper understanding of the different physiological responses among varieties under water stress. In this context, previous reports show an interplay between stomatal regulation of transpiration and changes in leaf hydraulic conductivity, also with the involvement of aquaporins (AQPs), particularly under water stress. However, how those signaling mechanisms are regulated in different grapevine varieties along phenological phases is unclear.

Impact assessment of the reverse osmosis technique in wine alcohol management

Wine authenticity and composition can be influenced by a range of membrane separation processes as reverse osmosis. In the context of climate change, the natural trend is to obtain wines with higher alcoholic concentration when classical winemaking methods are employed, and this may induce alteration of typicity of wines by masking the olfactory and taste properties. This study aimed to evaluate the influence of reverse osmosis techniques used for decrease of ethanol content on the stable isotopic ratios as markers for wine authenticity characteristics.

A GIS Analysis of New Zealand Terroir

This paper summarises a national survey of the geological setting of vineyards in New Zealand. We also provide an overview of climate, slope, aspect and varietals planted in New Zealand vineyards as a whole and for some individual regions.