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…

Dry leaf hyperspectral reflectance predicts leaf elemental composition in grafted hybrids

Elemental composition, measured as the concentrations of different elements present in a given tissue at a given time point, is a key indicator of vine health and development. While elemental composition and other high-throughput phenotyping approaches yield tremendous insight into the growth, physiology, and health of vines, costs and labor associated with repeated measures over time can be cost-prohibitive. Recent advances in handheld sensors that measure hyperspectral reflectance patterns of leaf tissue may serve as an affordable proxy for other types of phenotypic data, including elemental composition. Here, we ask if reflectance patterns of dried Chambourcin leaf tissue from an experimental grafting vineyard can predict the known elemental composition of those leaves.

Juice carbon isotope discrimination is related to vine growth and fruit quality of Barossa Shiraz

Aim: Interactions between soil, climate and management that modulate vine growth, yield and grape composition are strongly defined by vine water availability and nutrient uptake during the season. Carbon isotope discrimination (δ13C) has been used as an integrative measurement of vine water availability during the season, with the potential to identify spatial variations of terroir in

Capture depletion of grapevine DNA: an approach to advance the study of microbial community in wine

The use of next-generation sequencing (NGS) has helped understand microbial genetics in oenology. Current studies mainly focus on barcoded amplicon NGS but not shotgun sequencing, which is useful for functional analyses. Since the high percentage of grapevine DNA conceals the microbial DNA in must, the majority of sequencing data is wasted in bioinformatic analyses. Here we present capture depletion of grapevine whole genome DNA.

The importance of landscape in wine quality perception: l’importanza del paesaggio nella percezione qualitativa del vino

The wine quality is a characteristic that is both difficult to define and communicate, because the quality attributes can be divided into intrinsic (objective, such as alcohol degree, acidity

Functionality of different inter-stimulus rinse protocols for the sensory analysis of wildfire affected wines

From the effect of global climate change, wildfire occurrence during grape ripening has increased. These wildfires produce smoke that can carry organic compounds to a vineyard. These smoke compounds are adsorbed in the grape berry and result in wines with elevated levels of smoke-related phenols. These wines are described as having a smokey, burnt, and dirty aroma (Kristic et al, 2015). Not only are volatile phenols carried by smoke, but additionally glycoconjugate forms of these phenols are present as will. These have been found to have a large impact on the flavor of wines, being the cause of a lasting ashy aftertaste post consumption (Parker et al, 2012). When evaluating the sensory profile of these wines when tasted one after the other, there is an observed problem due to the lasting nature of these undesirable attributes and high level of carry-over from sample to sample. The aim of this work is to evaluate the extent this carryover occurs, along with the best sensory practices to mitigate its influence via different inter-stimulus rinse protocols.