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…

Drought responses in Chardonnay and Sauvignon blanc grapevine cultivars: Mechanistic insights and varietal contrasts

This study explored the responses of Chardonnay and Sauvignon blanc grapevine cultivars to water deficit across four years, uncovering their shared patterns and distinctive coping mechanisms. The research was conducted in a commercial vineyard located in Isla de Maipo, Chile. Various characterization approaches were employed including plant water potentials (), gas exchange measurements, shoot vulnerability curves, productivity assessments, and leaf cell water relations. Linear mixed models and sensitivity analyses were performed using various statistical methods to evaluate cultivar responses to water deficit. As the water deficit progressed, both cultivars displayed a parallel reduction in stomatal conductance, leaf turgor, and increased shoot embolism.

A combination of biotechnology tools and coopers elements for an alternative the addition of SO2 at the end of the malolactic fermentation in red wines or at the “mutage” for the “liquoreux” wines

In red wines the post-MLF SO2 addition is an essential event. It is also the case for the “mutage” during the elaboration of the “liquoreux”. At these moments SO2 plays an antimicrobial action and an antioxidant effect. But at current pH of wines, ensuring a powerful molecular SO2 has become very difficult. Recent work on Brettanomyces strains have also shown that some strains are resistant up to 1.2 mg / L of molecular SO2. It’s also the case of the some Saccharomuces or Zygosaccharomyces strains suitable to re-ferment “liquoreux” wines after the “mutage”.

Morphological image analysis for determining bunch grape characteristics: A case study on bunch weight in Cabernet-Sauvignon

Morphological image analysis is a powerful technique used in various fields, including agriculture, to quantitatively assess the physical characteristics of objects. In viticulture, the accurate assessment of grapevine characteristics is essential for optimizing crop management and improving the quality of wine production.

Viticultural Climatic Zoning and Digital Mapping of Rio Grande do Sul – Brazil, using Indices of the Géoviticulture MCC System

The State Rio Grande do Sul is the main producer of Brazilian fine wines, with four viticultural regions. The objective is the characterization of the viticultural climatic potential of the State (total surface of 281.749 km2). The methodology use the Géoviticulture Multicriteria Climatic Classification System (Géoviticulture MCC System), based on three climatic indices – Dryness Index (DI), Heliotermal Index (HI) and Cool Night Index (CI).

Spatial variability of the nutrient distribution in Jerez vineyard soils (Spain)

From a fertility standpoint, the vine has to extract from the soil mineral substances necessary for its existence. However, the amount of certain available nutrients does not always correspond to a proportional increase in quality.