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…

Low and zero alcohol “wines”: impact of different dealcoholization processes on phenol profile and health benefits

Consumers’ demand for non-alcoholic wine has notably increased in the last years: this trend is a consequence of a growing interest in more healthy habits, and as a response to higher alcohol levels in wine due to climate change. In addition, drinking limitations due to physiological/pathological conditions (e.g., pregnancy, diabetes, hepatic disorders), driving regulations, ethical/religious considerations, and high import taxes on alcoholic beverages have positively influenced this marked (us$ 1.6 billion in 2021). International organisation of vine and wine (OIV) established that alcohol content defining wines must not be less than 8.5% vol, (OIV, 2017).

Extraction of polyphenols from grape marc by supercritical fluid extraction (SFE) and evaluation of their ‘bioavailability’ as dietary supplements

In the winemaking process, several compounds that remain in the grape skins and seeds after the fermentation stage are bioactive-compounds (substances with potential beneficial effects on health) that can be extracted in order to recovery valuable substances with a high commercial value for the cosmetic, food (nutraceuticals) and pharmaceutical industries. The skins contain significant amounts of bioactive substances such as tannins (16-27%) and other polyphenolic compounds (2-6.5%) in particular, catechins, anthocyanins, proanthocyanins, quercetin , ellagic acid and resveratrol.

New antibacterial peptides produced by Saccharomyces cerevisiae responsible for the inhibition of malolactic fermentation

In winemaking, several antimicrobial peptides (AMPs) produced by different strains of Saccharomyces cerevisiae were found to be responsible for the inhibition of malolactic fermentation (MLF) carried out by some strains of Oenococcus oeni. However, only two AMPs produced by one of the yeast strains studied were totally identified and their mechanism of action was described. In an attempt to identify new AMPs, a 5-10 kDa peptidic fraction produced by an oenological strain of S. cerevisiae and previously shown to strongly inhibit MLF carried out by a strain of O. oeni was further purified.

CHARACTERIZATION OF ENOLOGICAL OAK TANNIN EXTRACTS BY MULTI-ANALYTICAL METHODS APPROACH

Oak tannin extracts are commonly used to improve wine properties. The main polyphenols found in oak wood extracts are ellagitannins¹ that release ellagic acid upon hydrolysis and comprise numerous structures². Moreover, oak tannin extracts contain other compounds giving a complex mixture. Consequently, the official OIV method based on gravimetric analysis of the tannin fraction adsorbed on polyvinylpolypyrrolidone is not sufficient to describe their composition and highlight their chemical diversity.

Current climate change in the Oplenac wine-growing district (Serbia)

Serbian autochthonous vine varieties Smederevka (for white wines) and Prokupac (for rosé and red wines) are the primary representatives of typical characteristics of wines and terroir of numerous wine-growing areas in Serbia. In the past, these varieties were the leading vine varieties, however, as the result of globalization of winemaking and the trend of consumption of wines from widely prevalent vine varieties, they were replaced by introduced international varieties. Smederevka and Prokupac vine varieties are characterized by later time of grape ripening, and relative sensitivity to low temperatures. Climate conditions can be a restrictive factor for production of high-quality grapes and wine and for the spatial spreading of these varieties in hilly continental wine-growing areas.
This paper focuses on the spatial analysis of changes of main climate parameters, in particular, analysis of viticultural bioclimatic indices that were determined for the purposes of viticulture zoning of wine-growing areas in the period 1961-2010, and those same parameters determined for the current, that is, referential climate period (1988-2017). Results of the research, that is, analysis of climate changes indicate that the majority of examined climate parameters in the Oplenac wine-growing district improved from the perspective of Smederevka and Prokupac vine varieties. These studies of climate conditions indicate that changes of analyzed climate parameters, that is, bioclimatic indices will be favorable for cultivation of varieties with later grape ripening times and those more sensitive to low temperatures, such as the autochthonous vine varieties Smederevka and Prokupac, therefore, it is recommended to producers to more actively plant vineyards with these varieties in the territory of the Oplenac wine-growing district.