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…

Effects of wine versus de-alcoholised wine on the microbiota-gut-brain axis in a tau-pathology murine model of Alzheimer’s disease

Alzheimer’s Disease (AD) is the most common disorder associated with cognitive impairment and the main cause of dementia globally. Multiple evidence in the last decade suggest that the gut microbiome plays an important role in the pathogenesis and progression of AD via the microbiota-gut-brain axis, a network wherein microbiome and the central nervous system crosstalk via endocrine, immune, neural, and microbial metabolites signalling pathways.

Influence of Potential Alcohol and pH Adjustment on Polyphenols and Sensory Characteristics of Red Wines Produced at Different Harvest Time Points

Wine quality is influenced by grape maturity, typically monitored by measuring sugar content and acidity.

Supramolecular approaches to the study of the astringency elicited by wine phenolic compounds

The objective of this study is to review the scientific evidences and to advance into the knowledge of the molecular mechanisms of astringency. Astringency has been described as the drying, roughing and puckering sensation perceived when some food and beverages are tasted (1). The main, but possibly not the only, mechanism for the astringency is the precipitation of salivary proteins (2,3). Between phenolic compounds found in red wines, flavan-3-ols are the group usually related to the development of this sensation. Other compounds, phenolic or not, like anthocyanins, polysaccharides and mannoproteins could act modifying or modulating astringency perception by hindering the interaction between flavanols and salivary proteins either because of their interaction with the flavanols or because of their interaction with the salivary proteins.

Design of microbial consortia to improve the production of aromatic amino acid derived compounds during wine fermentation

Wine contains secondary metabolites derived from aromatic amino acids (AADC), which can determine quality, stability and bioactivity. Several yeast species, as well as some lactic acid bacteria (LAB), can contribute in the production of these aromatic compounds. Winemaking should be studied as a series of microbial interactions, that work as an interconnected network, and can determine the metabolic and analytical profiles of wine. The aim of this work was to select microorganisms (yeast and LAB) based on their potential to produce AADC compounds, such as tyrosol and hydroxytyrosol, and design a microbial consortium that could increase the production of these AADC compounds in wines.

INTENSE PULSED LIGHT FOR VINEYARD WASTEWATER: A PROMISING NEW PROCESS OF DEGRADATION FOR PESTICIDES

The use of pesticides for vine growing is responsible for generating an important volume of wastewater. In 2009, 13 processes were authorized for wastewater treatment but they are expensive and the toxicological impact of the secondary metabolites that are formed is not clearly established. Recently photodecomposition processes have been studied and proved an effectiveness to degrade pesticides and to modify their structures (Maheswari et al., 2010, Lassale et al., 2014). In this field, Pulsed Light (PL) seems to be an interesting and efficient process (Baranda et al., 2017). Therefore, the aim of this work was to investigate the PL technology as a new process for the degradation of pesticides.