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…

MAPPING THE CONCENTRATIONS OF GASEOUS ETHANOL IN THE HEADSPACE OF CHAMPAGNE GLASSES THROUGH INFRARED LASER ABSORPTION SPECTROSCOPY

Under standard wine tasting conditions, volatile organic compounds (VOCs) responsible for the wine’s bouquet progressively invade the glass headspace above the wine surface. Most of wines being complex water/ethanol mixtures (with typically 10-15 % ethanol by volume), gaseous ethanol is therefore undoubtedly the most abundant VOC in the glass headspace [1]. Yet, gaseous ethanol is known to have a multimodal influence on wine’s perception [2]. Of particular importance to flavor perception is the effect of ethanol on the release of aroma compounds into the headspace of the beverage [1].

LARGE SURVEY OF THE CHEMICAL COMPOSITION OF WINES RESULTING OF THE PRESSING OF RED WINE MARC. FIRST RESULTS

In the Bordeaux vineyards, press red wine represents about 15% of the volume of wines. Valuing this large volume of press wine is necessary from an economic point of view, of course, but also because of their organoleptic contribution to the blend. Nevertheless, there is a lack of recent knowledge on the composition of press wines. This work aims to establish an initial assessment of their composition (aromatic and polyphenolic) and to set up hypothesis on to the links with their sensorial identity.

Characterization and modelling of water flow on vineyard soil. Effect of compaction and grass cover

In the Burgundy vineyard, frequent tractor traffic and management of inter-rows alternating grass cover and chemical weed-control lead to structural soil contrast between row and inter-row. The aim of this study was to characterize and model water flow in relation with topsoil structure modifications induced by these practices. Void ratio of the different soil volumes were determined using bulk density measurements.

High-throughput sequencing analysis based on nematode indices revealed healthier soils of organic vineyards 

Proper soil health assessments are crucial for sustainable cropland. Among the widely employed approaches, evaluating nematode community structure is particularly suitable. Traditionally, the taxonomic characterization of soil nematodes has relied on time-consuming morphology-based methods requiring experienced experts. However, molecular tools like high-throughput sequencing have emerged as efficient alternatives. In this study, we performed a metataxonomic analysis of soil samples collected from 57 vineyards in the DOCa Rioja region of Northern Spain, focusing on the impact of organic viticulture and cover cropping compared to integrated pest management (IPM) and tilling practices.

Enological potential of red grapes: cultivars and geographic origin of vineyards

The study of technologic and phenolic maturation is very efficient to determinate quality potential of red grapes cultivars and clones under different maturity levels or geographic origins