terclim by ICS banner
IVES 9 IVES Conference Series 9 Mobilizing endogenous transposable elements for grapevine improvement: a genomic and epigenomic approach in New Zealand Sauvignon Blanc

Mobilizing endogenous transposable elements for grapevine improvement: a genomic and epigenomic approach in New Zealand Sauvignon Blanc

Abstract

Efforts to improve the New Zealand wine industry’s climate resilience and sustainability through grapevine improvement are limited by germplasm availability and a reliance on Sauvignon Blanc exports. To address this, we are working to generate a population of 12,000 individuals with unique genetic traits, from which to select future clones for major export varieties.

Sauvignon Blanc plantlets are being regenerated from embryogenic callus, using an approach designed to mobilise endogenous transposable elements as mutagens. Alongside early phenotypic characterisation, whole-genome genotyping and epigenotyping is being conducted using nanopore sequencing. To facilitate this, we produced a phased diploid telomere-to-telomere (T2T) assembly of the clone progenitor. Each 500 Mb haplotype exhibits over 99% completeness and accuracy (QV ~60), with genic and repetitive elements annotated.

To evaluate the robustness of methylation signals to experimental parameters, we used low-coverage nanopore skim sequencing. Genomic and epigenetic variations in New Zealand’s commercial germplasm were similarly characterised. Preliminary analysis of the initial clone set promises insights into mutational processes operating in this collection, which we expect to be dominated by transposable element movement and epigenetic dysregulation.

This research aims not only to enrich the clonal diversity for future New Zealand viticulture but also to shed light on aspects of transposon mutagenesis, epigenetic variability, and the function of mutated genes. It is anticipated that these findings will contribute to crop improvement efforts both in New Zealand and internationally, by advancing the understanding of somatic variability and epigenomics in agriculture.

Download the abstract

DOI:

Publication date: June 13, 2024

Issue: Open GPB 2024

Type: Article

Authors

Darrell Lizamore1*, Annabel Whibley1, Bhanupratap Vanga1, Cen Liau1, Philippa Barrell2, Chris Winefield3, Solomon Wante1, Amy Hill1, Ellie Bradley1

1 Grapevine Improvement Team, Bragato Research Institute, Lincoln, New Zealand
2 Plant and Food Research Ltd., Lincoln, New Zealand
3 Dept. Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand

Contact the author*

Keywords

somatic mutations, transposable elements, nanopore sequencing, epigenetics

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

A zoning study of the viticultural territory of a cooperative winery in Valpolicella

The Valpolicella hilly area, north of Verona, is highly vocated for viticulture but its vineyards are sometimes characterized by very different soil and microclimate conditions which can greatly affect their oenological potential.

Read More

Function, barriers, and the environmental benefits of reuse bottle system for wine

With 0.3 to 0.7 kg CO2eq per 0.75 L wine, the glass bottle is the main contributor to the carbon footprint of a bottle of wine.

Read More

Toward an automatic way to identify red blotch infected vines from hyperspectral images acquired in the field

Vineyards are affected by different virus diseases, which can lower yield and affect the quality of grapes. Grapevine red blotch disease is one of them, and no curative solution exists. Once infected, a vine must be removed and replaced with a virus-free vine (aka roguing). Screening vineyards to look for symptoms can be time-consuming and needs well-trained experts. To improve this process, we conducted an experiment identifying infected vines using a hyperspectral camera in the field.

Read More

Control of microbial development in wines elaborated by carbonic maceration

Carbonic Maceration (CM) winemaking is typically used in different European regions. But It is paradoxical that being a traditional processing system and widely used in many wineries, some of the phenomena that take place and the parameters that characterize them are barely known. In this vinification system the intact grape clusters are placed in a carbon dioxide (CO2) enriched medium, and they immediately change from a respiratory metabolism to an anaerobic fermentative metabolism called intracellular fermentation, which is carried out by grape enzymes. But some grapes located in the lower zone of the tank are crushed by the weight of the ones above and release must, which is fermented by yeasts.

Read More

THE INFLUENCE OF COMMERCIAL SACCHAROMYCES CEREVISIAE ON THE POLY-SACCHARIDES AND OTHER CHEMICAL PROFILES OF NEW ZEALAND PINOT NOIR WINES

Wine polysaccharides (PS) play an important role in balancing mouthfeel and stability of wine and even influence aroma volatility. Despite this, there is limited research into the effect of winemaking additives on the polysaccharide profile and other macromolecules of New Zealand (NZ) Pinot noir wine. In this study the influence of a selection of commercial S. cerevisiae strains on the chemical profile, including polysaccharides, of New Zealand Pinot noir (PN) wine was investigated. Research scale PN fermentations using five strains of commercially available S. cerevisiae (Lalvin EC1118 and RC212, Levuline BRG YSEO, Viallate Ferm R71 and R82) were undertaken. PS were qualified and quantified using HPLC-RID.

Read More