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…

Monitoring of Pesticide Residues from Vine to Wine

Those previous years, pesticides are often brought to the forefront by media. Questions arose about their toxicity for growers and consumers. Even if a downward trend is underway, the use of pesticides is required to ensure steady quality and quantity of harvests. A large number of active ingredients are authorized but regarding viticulture, mainly insecticides and fungicides are applied, to control pests and diseases and to increase crop yield. Some phytosanitary products, principally fungicides, applied close to the harvest date may frequently be detected in wines.

Effect of ozone application for low-input postharvest dehydration of wine grapes 

The postharvest dehydration of grapes is a traditional practice to obtain wines with unique traits (e.g. sweet, dry/reinforced). The modern facilities (dehydrating rooms) used for this purpose are equipped with systems for artificially controlling the inside environment parameters, to obtain the desired dehydration kinetic and preserve the grapes from grey mold (Botrytis cinerea) infection, However, the conditioning systems are extremely energy-demanding and the identification and practical applications of solutions effective in controlling/reducing the postharvest decay would reduce the costs of the operation of the dehydration facilities. To this end, we explored the potential of ozone-based treatments on harvested grapes and preliminarily tested if the treatment could impact the normal behavior and metabolism of grapes during the traditionally slow dehydration practice.

Elucidating white wines peptides: An analytical breaktrough

The chemistry of wine is particularly complex due to biochemical and chemical interactions that significantly modify its organoleptic characteristics and stability over time. Aging on lees is a well-known practice during which various compounds are released, ensuring wines oxidative stability and its overall sensory quality [1,2].

Insulative effects of vine shelters may impact growth potential and cold hardiness of young vines

Context and purpose of the study. The seasons immediately following planting are key growth stages where young vines are particularly susceptible to various forms of damage.

Microbial consortia as a tool for sustainable vineyard management: A study on their acceptance among Veneto region’s grape-growers

Sustainability is a key focus in viticulture, where managing abiotic and biotic stress presents a major challenge.