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…

Effect of row direction in the upper part of the hillside vineyard of Somló, Hungary

Hillside vineyards have a great potential to produce world class wines. The unique microclimate lead to the production of rich, flavory wines.

Read More

Remote sensing and radiometric techniques applied to vineyards in two regions of Rio Grande do Sul, Brazil

The observation of Earth by satellites has demonstrated the feasibility of establishing differences between plant species, from their spectral features. The reflectance spectrum of vine plants follows this trend, being possible to identify vineyards in satellite images, among other species.

Read More

Evolution of grapeseed composition during maturation and characterization of its impact on wine compound using molecular networks

Usually the winemaker consider the grapeberry maturity as an actor of the wine quality. Grape seed are frequently used as a marker to assess the grape maturity. The first aim of this study is to obtain a better understanding of the impact of grape seed maturity on the grape seed and grape berry composition.

Read More

Isolation, biofilm formation and control of the wine spoilage yeast Brettanomyces bruxellensis

Brettanomyces bruxellensis, commonly referred to as “Brett,” is one of the most notorious microorganisms implicated in wine spoilage. This yeast species has developed a noteworthy resistance to sulfur dioxide, a widely used preservative in winemaking, prompting the wine industry to seek new antimicrobial agents.

Read More

CHEMICAL DRIVERS OF POSITIVE REDUCTION IN NEW ZEALAND CHARDONNAY WINES

According to winemakers, wine experts and sommeliers, aromas of wet stone, mineral, struck match and flint in white wines styles, such as those produced from Vitis vinifera L. cv. Chardonnay, are considered to be hallmarks of positive reduction.1,2 In recent years, the production of Chardonnay styles defined by aroma characteristics related to positive reduction has become more desirable among wine experts and consumers. The chemical basis of positive reduction is thought to originate from the concentration of specific volatile sulfur compounds (VSCs), including methanethiol (MeSH) imparting mineral and chalk notes,3 and benzenemethanethiol (BMT) responsible for struck match and flint.1,4

Read More