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.

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

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…

Determination of steviol glycosides in wine by HPLC

The SCL laboratory in Bordeaux is one of the two official control laboratories for wine and wine products in france, under the authority of the ministry of finance and two of its general directorates: the DGCCRF (directorate general for competition, consumer affairs and fraud control) and the DGDDI (directorate general of customs and excise duties). In this capacity, it verifies the regulatory compliance of wines and investigates any possible falsifications or fraud. Steviol glycosides are natural sweeteners that are not authorized as additives in wine.

Unraveling the complexity of high-temperature tolerance by characterizing key players of heat stress response in grapevine

Grapevine (Vitis spp.) is greatly influenced by climatic conditions and its economic value is therefore directly linked to environmental factors. Among these factors, temperature plays a critical role in vine phenology and fruit composition. In such conditions, elucidating the mechanisms employed by the vine to cope with heat waves becomes urgent. For the past few years, our research team has been producing molecular and metabolic data to highlight the molecular players involved in the response of the vine and the fruit to high temperatures [1]. Some of these temperature-sensitive genes are currently undergoing characterization using transgenesis approaches coupled or not with genome editing, taking advantage of the Microvine genotype [2].

Sensory characterisation and consumer perspectives of Australian Cabernet Sauvignon wine typicity

Aim: To identify the sensory attributes responsible for the typicity of Cabernet Sauvignon wines from three Australian Geographical Indications (GIs) and to explore consumer purchase behaviour and preference with regard to regional wines.

Clones of 10 Vitis vinifera varieties: degree of inter- and intra-varietal variation and putative mechanisms underlying clonal variability

Context and purpose of the study. Intra-varietal variability for key physiological and oenologically important traits can be exploit in viticulture following the consistently higher environmental pressure driven by climate change.

From protein-centered to gene-centered approaches to investigate DNA-protein interactions in grapevine

DNA-binding proteins play a pivotal role in critical cellular processes such as DNA replication, transcription, recombination, repair, and other essential activities. Consequently, investigating the interactions between DNA and proteins is of paramount importance to gain insights into these fundamental cellular mechanisms. Several methodologies have been devised to uncover DNA-protein interactions, which can be broadly categorized into two approaches. The “protein-centered” approach focuses on identifying the DNA sequences bound by a specific transcription factor or a set of TFs. Techniques falling within this category include chromatin immunoprecipitation, and protein-binding microarrays.