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…

“Compost Application in the Vineyard: Effects on Soil Nutrition and Compaction”

The mechanization of pruning and harvesting in vineyards has increased the risk of soil compaction. To reclaim soil properties or avoid this degradation process, it is crucial to properly manage the soil organic matter, and the application of compost derived from the vines themselves is a strategy to achieve this. The objective of this study was to evaluate the properties of soil treated with different doses of compost applied both on the vine row and the inter rows of a Vitis vinifera crop.

Zonazione dell’area viticola doc durello

Il lavoro di zonazione riveste un ruolo importante per capire le potenzialità e la vocazionalità di una specifica area viticola. La viticoltura dovrebbe essere vista in funzione dell’obiettivo enologico che si vuole realizzare e quindi particolare importanza riveste il risultato delle vinificazioni delle uve provenienti dai vigneti delle diverse aree della zona di produzione oggetto d’indagine. La zonazione dell’area a DOC Monti Lessini Durello ha preso in esame la varietà “Durella”, vitigno autoctono del territorio, che rappresenta la maggior parte della produzione vitivinicola della zona.

Correlations between N,S,O-heterocycle levels and age of Champagne base wines

Champagne regulation allows winegrowers to stock small amounts of still wines in order to compensate vintages’ quality shifts mainly due to climate variations. According to their technical requirements and house style some Champagne producers (commonly named “Champagne houses”) use these stored wines in the blend in order to introduce an element of complexity. These wines possess the particularity of being aged on fine lees in thermo-regulated stainless steel tanks. The Champagne house of Veuve Clicquot Ponsardin has several wines stored this way.

Impact of technical itineraries on the diversity and the functioning of arbuscular mycorrhizal fungi and associated microorganisms in vineyards soils and grapevine roots

Context and purpose. The vine is a holobiont, where the plant interacts positively, negatively, and neutrally with microbes that together form the vine’s microbiome.

VineAI: artificial intelligence for fungal disease

Early and accurate grapevine disease detection and surveillance are crucial for optimizing vineyard management practices.