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…

Vertical cordon training system enhances yield and delays ripening in cv. Maturana Blanca

The growing interest in minority grape varieties is due to their potential for adaptation to global warming and their oenological capabilities. However, the cultivation of these varieties has often been limited due to their low economic efficiency. One such example is Maturana Blanca, a recently recovered and authorized minority grape variety in the DOCa Rioja region, known for its remarkable oenological potential but low productivity. This study aimed to increase the yield of Maturana Blanca by implementing the vertical cordon training system, which allowed for a higher number of buds per plant and an increased cluster count per vine.

Read More

Callinikos: the new white table grapeseedless variety for biological produce

This paper presents is the create, the study and amplographic description the new seedless grape variety «Callinicos» was created by P. Zamanidis at the Athens Vine Department

Read More

Root water uptake patterns in rootstock-scion interactions influence grape water use strategies in a Mediterranean vineyard

Increasing drought is the most important impact of the ongoing climate change in the Mediterranean Basin, and it is predicted to result in productivity decreases and changes in grape quality.

Read More

Chitosan from sustainable source: antimicrobial activity against undesirable yeasts for production of low-sulphite wine

The addition of sulphur dioxide (SO2) is the method traditionally used for wine stabilisation, due to its broad spectrum of action against unwanted microorganisms and its ability to prevent oxidative phenomena.

Read More

Potentiel des sols viticoles et qualité des vins

La qualité des vins dépend de différents facteurs et procédés, notamment de la nature des terrains viticoles. Dans ce travail, nous avons cherché à établir les liens entre descripteurs pédologiques des parcelles et descripteurs sensoriels des vins. Sur la base de Classifications Ascendantes Hiérarchiques (CAH) et d’Analyses en Composante Principale (ACP), il a été possible d’établir des liens entre la nature des parcelles (sableuse, argileuse, sablo-graveuleuse) et certains descripteurs sensoriels des vins (chaleur, astringence, fruit noir) et plus globalement avec le type de vins élaborés.

Read More