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…

Clustering wine aromatic composition of Vitis vinifera grapevine varieties

Climate change is likely to impact wine typicity across the globe, raising concerns in wine regions historically renowned for the quality of their terroir. Amongst several changes in viticultural practices, replacing some of the planting material (i.e clones, rootstocks and cultivars) is thought to be one of the most promising potential levers to be used for adapting to climate change. But the change of cultivars also involves the issue of protecting the region’s wine typicity.

Read More

Addition of Malvasia di Candia Aromatica must and marcs to Golden Ale beer wort to obtain different Italian Grape Ales

Nowadays, the recovery of secondary resources of wine industry is insufficient and the developing of new products and adjuvants from secondary raw materials could become a relevant sector of research. The re-use of byproducts derived from winemaking could improve the sustainability of wine industry and give additional value to other food industries

Read More

Vine nitrogen status and the terroir effect: a study on cv. Doral in the Vaud vineyard (Switzerland)

A 3-year study was conducted in the Vaud vineyard (Switzerland) to evaluate the effects of « terroir » on the ecophysiology and fruit compostion of Vitis vinifera L. cv.

Read More

Volatile composition of base wines to obtain sparkling wines from seven autochthonous grape varieties from Castilla y León (Spain)

The aim of this work was to characterize the aromatic profile of white and rosé base wines for the elaboration of sparkling wines from seven autochthonous grape varieties of Castilla y León. The ‘Albarín’, ‘Godello’ and ‘Verdejo’ white grape cultivars contribute with more fruity notes than the ‘Viura’ and ‘Malvasía’ cultivars; and ‘Prieto picudo’ coloured grape cultivar has more fruity character than ‘Garnacha’.

Read More

Aroma profile of Oenococcus oeni strains in different life styles

AIM: Three Oenococcus oeni strains previously isolated from spontaneous malolactic fermentation were characterized for their surface properties. Planktonic and sessile cells were investigated for aroma compounds production and the expression of genes involved in citrate and malate metabolism (citE and mleA, respectively), glycoside-hydrolase (dsrO), fructansucrase (levO), rhamnosyl-transferase (wobB), glycosyltransferase (wobO).

Read More