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…

Les outils pour favoriser le renouvellement des générations en viticulture

French lawmakers have chosen the family-type winegrowing business as the benchmark for drafting the legal framework for winegrowing businesses and winegrowers. In france (source: msa), in 2022, there were 1,444 new winegrowers, an increase of 3% compared with 2021, representing 10% of new farm managers. The retention rate for winegrowers is 75% (up 13% on 2021), compared with 77% for all agricultural sectors (stable).

Use of chitosan as a secondary antioxidant in juices and wines

Chitosan is a polysaccharide produced from the deacetylation of chitin extracted from crustaceous and fungi. In winemaking chitosan is mainly used in the clarification of grape juice and wine, stabilization of white wines, removal of metals and to prevent wine spoilage by undesired microorganisms. The addition of chitosan to model wine systems was able to retard browning, reduce levels of metallic ions (Fe and Cu) and to protect varietal thiols due to its antiradical activity1. The present experiment was planned in order to evaluate the use of chitosan as a secondary antioxidant at three different stages of Sauvignon blanc fermentation and winemaking. Sauvignon blanc juices from three different locations were obtained at a commercial winery in Marlborough, New Zealand. One lots of grapes was collected from a receival bin and pressed into juice with a water-bag press, and a further juice sample was collected from a commercial pressing operation. Chitosan (1 g/L, low molecular weight, 75 – 85% deacetylated) was added to the juice after pressing, after cold settling, after fermentation, or at all these stages. Controls without any chitosan additions were also prepared.

Exploring the mechanisms of grapevine single berry development and ripening

The strategy of single berry phenotyping is a recently rediscovered research tool that has gained great attention. The latest studies have indicated that previous physiological models based on pooling asynchronous populations of berries provided biased or blurred information on berry development key players. The possibility of monitoring and sampling single synchronized berries to study their development sequentially has opened new lines of research aimed at unraveling the genes that regulate grapevine fruit development. This study aimed to decipher the gene pathways responsible for the activation/deactivation of physiological processes involved in the green phase of growth, the onset of ripening, and the second growth phase.

Regionality in Australian Shiraz: Sensory profiles of wines from six regions and their associations with chemical, geographical and climatic elements

Aim: Regional characters relating to Shiraz in Australia are not well documented. This study aimed to characterize the sensory, chemical and climate profiles of wines from various Australian Shiraz producing regions. 

Hierarchy of the interactions between physical and biological parameters intervening in the Pyrenean Gascon foothill vineyard

Un travail sur les A.O.C. du piémont pyrénéen occidental permet de construire une hiérarchie de paramètres climatiques, géo-pédologiques, morphologiques, de saisir leurs niveaux d’interaction et d’élaborer une méthodologie pour proposer un zonage