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…

Approaches for estimating the age of old vineyards in Campo de Borja

Determining the age of a vineyard is essential for understanding its influence on wine quality and characteristics.

Read More

2018 updates on the agronomic performances of fungus resistant wine grapes in Trentino (Italy)

On the market there are several wine grapes which are tolerant to the main fungal diseases. These varieties, commonly defined “resistant”, were developed in the grapevine breeding programs carried out mainly in Germany, France, Hungary and Italy. Some of these cultivars have been included in the national catalogues of wine grape varieties and have sometimes been allowed for specific kinds of wine. The VEVIR project, aimed at the enological evaluation of resistant vines, involves 33 cultivars achieved at the State Institute for Viticulture Freiburg in Germany, the Research Institute of Viticulture and Enology Pecs in Hungary and the Fondazione Edmund Mach S. Michele all’Adige (FEM) in Italy.

Read More

The FEM grapevine crossbreeding program for resistance to the main ampelopathies: towards climate-resilient varieties

The technique of crossing, whether free or controlled, has always been a source of variability allowing the selection of new varieties with improved fitness.

Read More

Mean polymerization degree of proanthocyanidins of grape seeds, skins and wines from Agiorgitiko (cv. Vitis vinifera): Differences among vintages

Grape phenolic compounds are very important constituents of red wine because, in addition to their antioxidant properties, they contribute to color, astringency and bitterness, oxidation reactions, interactions with proteins and ageing behavior of wines. The aim of our study was to assess the structural characteristics of grape and wine proanthocyanidins of Agiorgitiko variety and to evaluate the influence of the vintage year. Twelve vineyard locations were designated in the Nemea wine region. For three consecutive years (2012-2014), the grapes were harvested at technological maturity and the method of phloroglucinolysis was employed to determine the mean degree of polymerization (mDP) and subunit composition of the samples.

Read More

Influence of coinoculation of L. plantarum and O. oeni on the color and composition of Tempranillo wines

AIM: The aim of this research was to determine the influence of performing malolactic fermentation (MLF) of Tempranillo wines by coinoculation with Lactobacillus plantarum or Oenococcus oeni and Saccharomycescerevisiae on the composition and color of the final wines in comparison with sequential inoculation with Oenococcus oeni and spontaneous MLF. METHODS: Around 1500 Kg of Tempranillo grapes from Pagos de Anguix winery (Anguix, AOC Ribera de Duero, Spain) were harvested at the optimal maturity

Read More