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…

Comparing the chemical and sensory consequences of grapevine smoke exposure in grapes and wine from different cultivars and different wine regions in Australia

Aim: This study aimed to benchmark the chemical and sensory consequences of grapevine exposure to smoke, by comparing: (i) the concentration of volatile phenols and volatile phenol glycosides in control and smoke-affected grapes from different cultivars and different wine regions; and (ii) the chemical and sensory profiles of wines made from control and smoke-affected grapes, from different cultivars.  

Read More

Identification of 4-hydroxy-2-nonenal, a gamma nonalactone precursor in must and wine from Bordeaux cultivars

Various molecular compounds are responsible for the complex mixture of fragrances that give wine its aroma. In particular, the ‘cooked fruit’ aroma found in red wines from hot and/or dry vintages or from the vinification of late harvested grapes has been intensively investigated in recent years. Lactones and especially γ-nonalactone were found to be responsible for the ‘cooked fruit’

Read More

Winemaking options for the improvement of the attributes of the wines from grapes with different oenological potential and sanitary status

The aim of this work was to study winemaking alternatives that will optimize the quality of the Tannat wines, taking advantage of the grape’s oenological potential.

Read More

OPTIMIZATION OF EXTRACTION AND DEVELOPMENT OF AN LC-HRMS METHOD TO QUANTIFY GLUTATHIONE IN WHITE WINE LEES AND YEAST DERIVATIVES

Glutathione is a natural tripeptide composed of l-glutamate, l-cysteine and glycine, found in various foods and beverages. In particular, glutathione can be found in its reduced (GSH) or oxidized form (GSSG) in must, wine or yeasts¹. Numerous studies have highlighted the importance of GSH in wine quality and aging potential². During winemaking, especially during aging on lees, GSH helps prevent the harmful effects of oxidation on the aroma of the wine³. Nevertheless, the amounts of GSH/GSSG present in wine lees are often unknown and the choice of operating conditions (quantity of lees and aging time) remains empirical.

Read More

Pierce’s disease of grapevines, a new threat to the wine industry in Southern Europe

Pierce’s disease (PD) is considered a potential threat to european viticulture (EPPO a2 list of pathogens since 1981). In the usa, infections caused by the vector-borne bacterium xylella fastidiosa have caused recurrent damage to vineyards in California and the southeastern states. However, vineyards in Europe have remained free of PD until recently, when it was first detected on the island of Mallorca in 2017. The reasons for the absence of PD in continental Europe have not been convincingly explained.

Read More