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…

IMPACT OF METSCHNIKOWIA PULCHERRIMA DURING FERMENTATION ON AROMATIC PROFILE OF VIDAL BLANC ICEWINE

Non-Saccharomyces yeasts not only increase microbial diversity during wine fermentation, but also have a positive effect on improving wine aroma. Among these non-Saccharomyces yeast species, Metschnikowia pulcherrima is often studied and used in winemaking in recent years, but its application in icewine has been rarely reported. In this study, indigenous M. pulcherrima strains and Saccharomyces cerevisiae strains (commercial and indigenous strains) were sequentially inoculated for icewine fermentations; meanwhile, pure S. cerevisiae fermentations were used as the control; indigenous strains used above were screened from spontaneous fermentations of Vidal blanc icewine.

Antociani ed acidi cinnamici per la caratterizzazione di vitigni in zone diverse della Toscana

The phenolic compounds (cathechins, cynnamic acids, anthocyanidins) in wines made from 6 vine-varieties (Sangiovese, Cabernet S., Nero d’Avola, Foglia Tonda, Pinot N., Mazzese) grown in 4 different pedoclimatic zones of Tuscany (Arezzo, Grosseto, Pisa and Lucca) have been analyzed by HPLC.

Use of the soils information system for detailed vineyard soil surveys and as a component of precision viticulture

Vineyard soil surveys can be costly and time consuming. The Soils Information System (SIS) provides a set of tools to do a quick evaluation of soil physical properties in the vineyard. First, a system equipped with GPS and EM38 equipment, provides a very precise DEM and a soil electrical conductivity map. Specific sampling points are located for a tractor-mounted geotechnical probe to make soil physical measurements.

Methyl Jasmonate Versus Nano-Methyl Jasmonate: Effect On The Stilbene Content In Monastrell Variety

Stilbenes, a kind of non-flavonoid phenolic compounds, have been reported to be responsible for various beneficial effects. Their biological properties include antibacterial and antifungal effects, as well as cardioprotective, neuroprotective and anticancer actions (Guerrero et al. 2009).Several strategies can be used to increase stilbene content in grapes and one of them could be the use of elicitors such as methyl jasmonate. The use of this elicitor has been proven to be efficient in the production of secondary metabolites which increases the quality of wines, but its use also has some drawbacks such as its low water solubility, high volatility, and its expensive cost (Gil-Muñoz et al. 2021).

Phenology and bioclimate of grapevine varieties in the tropical region of the São Francisco Valley, Brazil

La région de la Vallée du São Francisco, situe à 9º S, est en train d’augmenter la production des vins fins les dernières années. La région présente climat du type tropical semi-aride (climat viticole à variabilité intra-annuelle selon le Système CCM Géoviticole : “très chaud, à nuits chaudes et à sécheresse forte à sub-humide” en fonction