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…

The influence of climate on the grapevine phenology and content of sugar and total acids in the must

For the period of 10 years in the condition of Skopje vineyard area, at two regional (Vranec and Smederevka) and two international (Cabernet sauvignon and Chardonnay) grapevine cultivars, the researches are done.

Amino nitrogen content in grapes: the impact of crop limitation

As an essential element for grapevine development and yield, nitrogen is also involved in the winemaking process and largely affects wine composition. Grape must amino nitrogen deficiency affects the alcoholic fermentation kinetics and alters the development of wine aroma precursors. It is therefore essential to control and optimize nitrogen use efficiency by the plant to guarantee suitable grape nitrogen composition at harvest. Understanding the impact of environmental conditions and cultural practices on the plant nitrogen metabolism would allow us to better orientate our technical choices with the objective of quality and sustainability (less inputs, higher efficiency). This trial focuses on the impact of crop limitation – that is a common practice in European viticulture – on nitrogen distribution in the plant and particularly on grape nitrogen composition. A wide gradient of crop load was set up in a homogeneous plot of Chasselas (Vitis vinifera) in the experimental vineyard of Agroscope, Switzerland. Dry weight and nitrogen dynamics were monitored in the roots, trunk, canopy and grapes, during two consecutive years, using a 15N-labeling method. Grape amino nitrogen content was assessed in both years, at veraison and at harvest. The close relationship between fruits and roots in the maintenance of plant nitrogen balance was highlighted. Interestingly, grape nitrogen concentration remained unchanged regardless of crop load to the detriment of the growth and nitrogen content of the roots. Meanwhile, the size and the nitrogen concentration of the canopy were not affected. Leaf gas exchange rates were reduced in response to lower yield conditions, reducing carbon and nitrogen assimilation and increasing intrinsic water use efficiency. The must amino nitrogen profiles could be discriminated as a function of crop load. These findings demonstrate the impact of plant balance on grape nitrogen composition and contribute to the improvement of predictive models and sustainable cultural practices in perennial crops.

INFLUENCE OF THE THICKNESS OF OAK ALTERNATIVES ON THE COMPOSITION AND QUALITY OF RED WINES

Aging red wines in oak barrels is an expensive and laborious process that can only be applied to wines with a certain added value. For this reason, the use of oak alternatives coupled with micro-oxygenation has progressively increased over recent years, because it can reproduce the processes taking place in the barrels more economically and quickly [1]. Several studies have explored how oak alternatives [2-5] can contribute to wine composition and quality but little is known about the influence of their thickness.

Global warming effects on grape growing climate zones within the Rioja Appllation (DOCa Rioja) in north Spain

Aims: The aims of this work were (1) to assess the changes in some of the main bioclimatic indices used for climate viticultural zoning within the Rioja Appellation area in the north of Spain between 1950-2014 (60 years), and (2) to carry out a comprehensive sociological evaluation among grapegrowers and winemakers of this region, to better understand the impact of climate change on their activity, their degree of concern about it and the potential adaptation measures they would be willing to adopt to cope with it in future years.

Chemical affinity and binding capacity between pre-purified Cabernet-Sauvignon/Merlot anthocyanins and salivary proteins monitored by UHPLC Q-ToF MS analysis

Apart from pro(antho)cyanidins and tannins, other phenolic compounds in wine or grapes have been shown to interact with salivary proteins and may contribute to overall sensory in-mouth sensations [1, 2]. Anthocyanins are the dominant phenolics in red wine and grape skin [3] , so it is expected that they come into contact and interact with salivary proteins after ingestion.