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…

Composition and biological potential of grape and wine phenolic compounds

Polyphenols are common in human diets, primarily in plant-derived food and beverages. They influence multiple sensory properties such as aroma, flavour, colour, and taste, such as astringency and bitterness [1]. The major phenolic compounds in grapes and wines are anthocyanins and tannins (proanthocyanidins or condensed tannins).

Study of the impact of nitrogen additions and isothermal temperature on aroma production in oenological fermentation

Nitrogen and temperature are two important factors that influence wine fermentation and volatile compounds production. Among the different compounds present in the must, nitrogen is an essential nutrient for the management of the fermentation kinetics but it also plays an important role in the synthesis of fermentative aromas. To address the problems related to nitrogen deficiencies, nitrogen additions during alcoholic fermentation have been developed.

Model-assisted analysis of the root traits underlying RSA genotypic diversity in Vitis: a promising approach for rootstock selection?

By dissecting the root system architecture (RSA) into its underpinning components (e.g. root emission, axial growth, radial growth, branching, root direction or tropism) and identifying the relationships between them, functional-structural 3D root models are promising tools for analyzing the diversity and complexity of root system phenotypes with Genotype × Environment interactions. The model parameters are assumed to be synthetic traits, less influenced by the environment, and consequently with less polygenic architectures than the integrative RSA traits they drive. Root models can serve as a basis for in silico development of root system ideotypes by highlighting the developmental processes and parameters that most likely influence RSA fitness.

Riesling as a model to irrigate white wine grape varieties in arid climates

Regulated deficit irrigation (RDI) is a common viticultural practice for wine grape production. In addition to the potential improvement of water use efficiency, the adoption of this technique favors smaller canopies with higher levels of fruit sun exposure, enhancing quality attributes associated with red wine grapes such as smaller berries with higher tannins and anthocyanins. However, these quality attributes do not necessarily transfer to white wine grapes. The goal of this project was to assess whether partial rootzone drying (PRD) is more suited than RDI to grow high-end white wine grapes in arid climates, especially aromatic varieties, using Riesling as a model.

Within-vineyard spatial variation impacts methoxypyrazine accumulation in the rachis of Cabernet-Sauvignon

To investigate the impact of spatial variation in vine vigour on the accumulation of methoxypyrazines in the rachis of Cabernet-Sauvignon. Cabernet-Sauvignon rachis has been shown to contain significantly higher concentrations