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…

Challenges for the Implementation of commercial inoculum of arbuscular fungi in a commercial Callet vineyard (Vitis vinifera L.)

Over the past 70 years, scientific literature has consistently illustrated the advantageous effects of arbuscular mycorrhiza fungi (AMF) on plant growth and stress tolerance. Recent reviews not only reaffirm these findings but also underscore the pivotal role of AMF in ensuring the sustainability of viticulture. In fact, various companies actively promote commercial inoculants based on AMF as biofertilizers or biostimulants for sustainable viticulture. However, despite the touted benefits of these products, the consistent effectiveness of AMF inoculants in real-world field conditions remains uncertain.

Are Farm to fork strategy goals reasonable and achievable? State of the art of Península de Setubal’s winegrowers

The European Union’s “farm to fork” strategy sets out several objectives to be achieved by farmers, who, among others, relate to increasing biodiversity, protecting soils and reducing the use of pesticides. At a time when the amendments to the national plans of Sustainable Use of pesticides are being discussed, it is important to understand what the Setúbal Peninsula region status is.

Use of new tools for red wine aging: active and passive microoxygenation with oak wood. Effect on volatile compounds and sensorial impact

The aim of this study was to evaluate the evolution of different chemical parameters and sensory impact on red wine during maturation in barrels or with new technologies

Estudio de la fertilidad de los suelos para la zonificación vitícola de la D.O. MONTILLA-MORILES

La D.O. Montilla-Moriles, situada en el sur de la provincia de Córdoba, corresponde a una de las zonas de mayor interés dentro de la vitivinicultura andaluza. Las formaciones de suelos

Evolution of the appellation of origin concept in the vineyards of Australia

Australia is the seventh largest producer of wine and crushed 1.42 million tonnes of wine grapes in the 2001 vintage.