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…

Ecophysiological performance of Vitis rootstocks under water stress

The use of rootstocks tolerant to soil water deficit is an interesting strategy to cope with limited water availability. Currently, several nurseries are breeding new genotypes, but the physiological basis of its responses under water stress are largely unknown. To this end, an ecophysiological assessment of the conventional 110-Richter (110R) and SO4, and the new M1 and M4 rootstocks was carried out in potted ungrafted plants. During one season, these Vitis genotypes were grown under greenhouse conditions and subjected to two water regimes, well-watered and water deficit. Water potentials of plants under water deficit down to < -1.4 MPa, and net photosynthesis (AN) <5 μmol m-2 s-1 did not cause leaf oxidative stress damage compared to well-watered conditions in any of the genotypes. The antioxidant capacity was sufficient to neutralize the mild oxidative stress suffered. Under both treatments, gravimetric differences in daily water use were observed among genotypes, leading to differences in the biomass of root, shoot and leaf. Under well-watered conditions, SO4 and 110R were the most vigorous and M1 and M4 the least. However, under water stress, SO4 exhibited the greatest reduction in biomass while M4 showed the lowest. Remarkably, under these conditions, SO4 reached the least negative stem water potential (Ψstem), while M1 reduced stomatal conductance (gs) and AN the most. In addition, SO4 and M1 genotypes also showed the highest and lowest hydraulic conductance values, respectively. Our results suggest that there are differences in water use regulation among genotypes, not only attributed to differences in stomatal regulation or intrinsic water use efficiency at the leaf level. Therefore, because no differences in canopy-to-root ratio were achieved, it is hypothesized that xylem vessel anatomical differences may be driving the reported differences among rootstocks performance. Results demonstrate that each Vitis rootstock differs in its ecophysiological responses under water stress.

Exploring changes in browning kinetics, color, and antioxidants due to dealcoholization of wine

The global consumer demand for low or non-alcoholic wine is growing steadily in recent years, driven by health concerns, religious beliefs, and personal taste preferences etc.. Consequently, the removal of alcohol from wine can significantly alter its chemical and sensory properties, including color, aroma, and taste, which make a significant challenge for consumer to accept these products. Ethanol plays a crucial role in various chemical reactions and interactions that contribute to the development of wine’s characteristics.

Understanding colloidal instability in white wine model solutions: A study focused on the effect of polysaccharides and salts onto bentonite efficiency

A white wine model solution (12% v/v ethanol, 4 g/L tartaric acid, pH 3.2) was used to assess wine colloidal instability as well as the influence of several wine components on bentonite performance in protein removal.

Technological possibilities of grape marc cell walls as wine fining agent. Effect on wine phenolic composition

Fining is a technique that is used to remove unwanted wine components that affect clarification, astringency, color, bitterness, and aroma. Fining involves the addition of adsorptive or reactive material in order to reduce or eliminate the presence of certain less desirable wine components and to ensure that a wine remains in a particular stable state for a given period of time Recently concerns have been raised about the addition of animal proteins, such as gelatin, to wine due to the disease known as bovine spongiform encephalopathy (Mad Cow disease). Although the origin of gelatins has been moved to porcine, winemakers are asking for substitute products with properties and application protocols similar to the traditional animal-derived ones, making the use of plant-derived proteins in fining a practically viable possibility. As a consequence, various fining agents derived from plants have been proposed, including proteins from cereals, legumes, and potato.

Identifying research opportunities at Douro Demarcated Region

The Douro Demarcated Region, in Northern Portugal, offers outstanding wines with unique characteristics. Due to the today’s globalized marketplace, local producers often need to further develop their cultivation techniques to remain competitive. The Association of Viticultural Development in the Douro Valley (ADVID) works as a unit of experimentation, offering services and training to meet the demands of the Douro’s vitiviniculturists.