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…

Heatwaves and grapevine yield in the Douro region, crop model simulations

Heatwaves or extreme heat events can be particularly harmful to agriculture. Grapevines grown in the Douro winemaking region are particularly exposed to this threat, due to the specificities of the already warm and dry climatic conditions. Furthermore, climate change simulations point to an increase in the frequency of occurrence of these extreme heat events, therefore posing a major challenge to winegrowers in the Mediterranean type climates. The current study focuses on the application of the STICS crop model to assess the potential impacts of heatwaves in grapevine yields over the Douro valley winemaking region. For this purpose, STICS was applied to grapevines using high-resolution weather, soil and terrain datasets over the Douro. To assess the impact of heatwaves, the weather dataset (1989-2005) was artificially modified, generating periods with anomalously high temperatures (+5 ºC), at certain onset dates and with specific durations (from 5 to 9 days). The model was run with this modified weather dataset and results were compared to the original unmodified runs. The results show that heatwaves can have a very strong impact on grapevine yields, strongly depending on the onset dates and duration of the heatwaves. The highest negative impacts may result in a decrease in the yield by up to -35% in some regions. Despite some uncertainties inherent to the current modelling assessment, the present study highlights the negative impacts of heatwaves on viticultural yields in the Douro region, which is critical information for stakeholders within the winemaking sector for planning suitable adaptation measures.

Vertical temperature gradient in the canopy provides opportunities to adapt training system in a climate change context

Aims: The aims of this study were (1) to measure the vertical temperature gradient in the vine canopy in parcels with different vineyard floor management practices and (2) to analyze the factors influencing this gradient. The objective was to investigate whether the increase of trunk height could be an adaptation strategy to reduce air temperature in the bunch zone in a context of climate change. 

Chemical and sensory profile of Brazilian red wines upon the cultivar and geographic origin of vineyards

Many vineyards implanted in Brazil in the last 20 years are placed under very different natural conditions if compared to Serra Gaúcha, the oldest and more traditional viticultural region in the country.

Nitrogen forms and Iron deficiency: how do Grapevine rootstocks responses change?

Grapevine rootstocks provide protection against environmental biotic and abiotic stresses. Nitrogen (N) and iron (Fe) are growth-limiting factors in many crop plants due to their effects on the chlorophyll and photosynthetic characteristics. Iron nutrition of plants can be significantly affected by different nitrogen forms through altering the uptake ratio of cations and anions, and changing rhizosphere pH. The aim of this study was to investigate the response mechanisms of grapevine rootstocks due to the interaction between different nitrogen forms and iron uptake.

Petiole phosphorus concentration is controlled by the rootstock genetic background in grapevine: is this a key for understanding rootstock conferred vigour?

Grapevine, Vitis vinifera, requires grafting on Phylloxera tolerant rootstocks of American origin in most viticultural areas of the world. The most commonly used species in rootstock creation are V. berlandieri, V. riparia and V. rupestris. Rootstocks not only provide tolerance to Phylloxera but assure the supply of water and mineral nutrients to the scion. The objective of this work was to determine to what extent rootstocks of different parentages alter the mineral composition of petioles of grapevine.