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…

Greffadapt: a relevant experimental vineyard to speed up the selection of grapevine rootstocks

[lwp_divi_breadcrumbs home_text="IVES" use_before_icon="on" before_icon="||divi||400" module_id="publication-ariane" _builder_version="4.20.4" _module_preset="default" module_text_align="center" module_font_size="16px" text_orientation="center"...
Read More

Methoxypyrazine concentrations in grape-bunch rachis are influenced by rootstock, region, light, and scion.

Methoxypyrazines (MPs) are readily extracted from grape berry and rachis during fermentation and can impart “green” and “herbaceous” sensory attributes to wine. Irrespective of whether MPs, including 3-isobutyl-2-methoxypyrazine (IBMP), 3-isopropyl-2-methoxypyrazine (IPMP), and 3-sec-butyl-2-methoxypyrazine (SBMP), are extracted from berry or other vine material, techniques for remediation of wine with overpowering sensory characters attributable to MPs suffer from poor specificity or produce undesirable sensory outcomes, meaning that alternative control approaches are needed.

Read More

On the stability of spectral features of four vine varieties in Brazil, Chile and France

Satellite images of vineyards in France, Chile, and Brazil are used to study spectral differences between the vine varieties Cabernet Sauvignon, Merlot, Pinot Noir, and Chardonnay, to verify if features of a given variety are conserved at vineyards in completely different terroirs.

Read More

Proteomic and activity characterization of exocellular laccases from three Botrytis cinerea strains

Botrytis cinerea is a fungus that causes common infection in grapes and other fruits. In winemaking, its presence can be both considered desirable in the case of noble rot infection or undesirable when grey rot is developed. This fungus produces an extracellular enzyme known as laccase which is able to cause oxidation of phenolic compounds present in must and wine, causing most of the times a decrease in its quality and problems during the winemaking process [1]. Material and methods: Three B. cinerea strains (B0510, VA612 and RM344) were selected and grown in a liquid medium adapted from one previously described [2]. The enzyme was isolated by tangential ultrafiltration of the culture medium using a QuixStand system equipped with a 30 KDa filtration membrane.

Read More

Influence of the temperature of the prise de mousse on the effervescence and foam of Champagne and sparkling wines.

The persistence of effervescence and foam collar during a Champagne or sparkling wine tasting constitute one, among others, specific consumer preference for these products. Many different factors related to the product or to the tasting conditions might influence their behavior in the glass

Read More