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…

The Albariño route in Uruguay: A clonal selection process to produce quality wines

In recent years, Uruguay has embraced the Albariño grape variety (Vitis vinifera L.) as one of the most promising for commercial growth. Originally cultivated in Galicia and northern Portugal, Albariño has risen to prominence in the global wine market, driving strong demand and significantly increasing grape prices [1].

Effects of Silver Thiosulphate and Salicylic Acid on the long-term maintenance of the embryogenic callus of Vitis vinifera

New Plant Breeding Techniques (NPBTs) have the potential to revolutionize the genetic improvement of grapevine. However, the practical application of these techniques is limited by several challenges, such as the difficulty in generating embryogenic calluses, maintaining their competence during in vitro cultivation, and regenerating plants without defects. To overcome these challenges, we conducted a study to test the effect of two treatments on callus cultures derived from different grapevine varieties, with and without embryogenic competence. The tested substances were Silver Thiosulphate (STS) an ethylene inhibitor, and Salicylic Acid (SA), an elicitor with different effects depending on the concentration of use beyond the ethylene inhibitor activity.

ENRICHMENT OF THE OENOLOGICAL MALDI-TOF/MS PROTEIN SPECTRA DATABASE FOR RELIABLE OENOLOGICAL YEAST AND BACTERIA IDENTIFICATION

The Matrix Assisted Laser Desorption/Ionization–Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) technology is commonly used in food and medical sector to identify yeast or bacteria species isolated from a nutritive culture media. Since a decade, brewery and oenology industries have been attracted to this method which combines fast analysis times, reliability and low cost of analysis. Briefly, this method is based on the comparison of the MALDI-TOF/MS protein spectra of an isolated colony of yeast or bacteria with those contain in a manufacturer’s reference protein spectra database. Initiated in 2015, the creation of the first oenological mass spectra database has proved to be essential for increase quality of species identification.

Oak wood influence on the organoleptic perception of red wine

Some wood substances such as ellagitannins (vescalagin, castalagin, grandinin, roburins (A, B, C, D, E)…) can be extracted during wine ageing in oak barrels. The level of these hydrolysable tannins in wine depends of the species and origin of oak wood as well as its treatment during barrel realization.

Bunch placement effects on dehydration kinetics and physico-chemical composition of Nebbiolo grapes

Sforzato di Valtellina DOCG is a special reinforced red wine produced using withered Nebbiolo grapes. The withering process takes place in traditional rooms under natural environmental conditions; it starts immediately after the harvest and ends not before the 1st December of the same year. The process can be performed with different bunch placements that can influence the grapes features.The purpose of the study is to compare the effect on grape physico-chemical parameters for four withering bunch placement systems: hanged clusters (HC), plastic crates (CT), breathable mesh fabric on wooden frames panels (MF), and reed mats (RM). For all the systems studied, the withering length was two months at a temperature between 6 and 19 °C and a relative humidity of 41-88%.