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…

Distinguishing of red wines from Northwest China by colour-flavour related physico-chemical indexes

Aim: Northwest China occupies an important position in China’s wine regions due to its superior geographical conditions with dry climate and sufficient sunlight. In this work, we aimed to investigate the physico-chemical colour and flavour characteristics of red wine in Northwest China.

Read More

How do KOCs influence wine consumers’ decisions? Based on NLP analysis and questionnaire surveys on Xiaohongshu

In China’s social media-driven marketing landscape, user-generated content (UGC) plays a pivotal role in brand communication and consumer decision-making.

Read More

Are all red wines equals regarding their vulnerability to Brettanomyces bruxellensis ?

Odours deemed harmful by the consumer and described as “stable”, “horse sweat” or “burnt plastic” can be found in wines. The responsible molecules are volatile phenols, produced by a spoilage yeast: brettanomyces bruxellensis. This species is particularly well adapted to the wine environment and can resists many stresses such as a high alcohol level, a low ph or high levels of SO2, more or less efficiently depending on the strain considered.

Read More

POTENTIAL OF PEPTIDASES FOR AVOIDING PROTEIN HAZES IN MUST AND WINE

Haze formation in wine during transportation and storage is an important issue for winemakers, since turbid wines are unacceptable for sale. Such haze often results from aggregation of unstable grape proteinaceous colloids. To date, foreseeably unstable wines need to be treated with bentonite to remove these, while excessive quantities, which are often required, affect the wine volume and quality (Cosme et al. 2020). One solution to avoid these drawbacks might be the use of peptidases. Marangon et al. (2012) reported that Aspergillopepsins I and II were able to hydrolyse the respective haze-relevant proteins in combination with a flash pasteurisation. In 2021, the OIV approved this enzymatic treatment for wine stabilisation (OIV-OENO 541A and 541B).

Read More

Influence of weather and climatic conditions on the viticultural production in Croatia

The research includes an analysis of the impact of weather conditions on phenological development of the vine and grape quality, through monitoring of four experimental cultivars (Chardonnay, Graševina, Merlot and Plavac mali) over two production years. In each experimental vineyard, which were evenly distributed throughout the regions of Slavonia and The Croatian Danube, Croatian Uplands,

Read More