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…

Influence of maceration time and temperature on some bioactive compounds in Malvazija istarska white wines

The rising trend of moderate wine consumption as a part of a healthy lifestyle promotes white wines with higher phenolic content because of their bioactive properties. Duration and temperature of the maceration process have a marked impact on the content and composition of wine phenolics. The aim of this study was to explore the effect of applying maceration processes of different durations and temperature on total phenolic content and flavan-3-ol compounds concentration of Malvazija istarska (Vitis vinifera L.) wines, an autochthonous Croatian white grape variety. Vinification took place at the Institute of Agriculture and Tourism (Poreč) where pre-fermentative two days cryomaceration treatment at 8 °C (CRYO), seven days maceration treatment at 16 °C (M7), and prolonged post-fermentative maceration treatments at 16 °C for 14 days (M14), 21 day (M21), and 42 days (M42) were studied and compared to non-maceration control treatment (C). Total phenolic content was determined by the Folin-Ciocalteu colorimetric method using a UV/VIS spectrophotometer and the results were expressed as gallic acid equivalents (mg/L GAE).

Spectral characterisation of fungal diseases on Vitis vinifera leaves

Aims: The aims of this study were to (1) detect alterations in the reflectance spectra of vines with fungal diseases, (2) map these alterations, and (3) determine the best wavelengths which may be used as early indicators of fungal diseases in vines.

Influence of inactive dry yeast treatments during grape ripening on postharvest berry skin texture parameters and phenolic compounds extractability

Inactive dry yeast treatments in the vineyard are a tool used with the aim to improve the concentration and quality of secondary metabolites in grapes, leading to a better differentiation of the wines made from grapes differently treated. In this work, a foliar spraying treatment with yeast derivatives specifically designed to be used with the patent pending application technology of Lallemand Inc. Canada (LalVigne® Mature, Lallemand Inc., Montreal, Canada) was tested on Vitis vinifera L. cv. Barbera and Nebbiolo black winegrapes. The aim was to evaluate the effect of this treatment on the phenolic compounds accumulation, the skin physical-mechanical properties and the related phenolic extractability. Prior to analysis, the berries were sorted by flotation in order to evaluate their distribution by density class, and to determine the skin texture parameters of berries with different sugar contents, thus understanding also the ripening effect.

An overview of geological influences on South African vineyards

The role of soils and bedrock geology has long been acknowledged as a fundamental component of terroir. In South Africa the influence of geology is misunderstood and some important geological components will be highlighted in this paper.

Impact of elemental sulfur (S0) residues in Sauvignon blanc juice on the formation of the varietal thiols 3-mercapto hexanol and 3-mercaptohexyl acetate

Elemental sulfur is a fungicide used by grape growers to control the development of powdery mildew, caused by the fungus Erysiphe necator. This compound is effective, cheap and has a low toxicity with no withholding period recommended. However, high levels of S0 residues in the harvested grapes can lead to the formation of reductive sulfur compounds that can impart taints and faults to the wine. Hydrogen sulphide (H2S) is a very volatile and unpleasant sulfur compound which formation is connected to high residues of S0 in juice (10 – 100 mg/L).