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…

Winemaking processes discrimination by using qNMR metabolomics

AIM: Metabolomics in food science has been increasingly used over the last twenty years. Among the tools used for wine, qNMR has emerged as a powerful tool to discern wines based on environmental factors such as geographical origin, grape variety and vintage (Gougeon et al., 2019a).

Read More

Grapevine bud fertility under elevated carbon dioxide

Aims: Microscopic bud dissection is a common tool used to assess grapevine bud fertility and therefore to predict the yield of the following season

Read More

Observation and modeling of climate at fine scales in wine-producing areas

Global change in climate affect regional climates and hold implications for viticulture worldwide. Despite numerous studies on the impact of projected global warming on different regions

Read More

NEW METHOD FOR THE QUANTIFICATION OF CONDENSED TANNINS AND OTHER WINE PHENOLIC COMPOUNDS USING THE AUTOMATED BIOSYSTEMS SPICA ANALIZER

Wine phenolic compounds are important secondary metabolites in enology due to their antioxidant and nutraceutical properties, and their role in the development of color, taste, and protection of wine from oxidation and spoilage. Tannins are valuable phenolic compounds that contribute significantly to these wine properties, especially in mouthfeel characteristics; however, tannin determination remains a significant challenge, with manual and time-consuming methods or complex methodologies. The purpose of this study is to propose a novel method for quantifying condensed tannins in finished wine products.

Read More

Water deficit impacts grape development without dramatically changing thiol precursor levels

The use of new fungus disease-tolerant grapevine varieties is a long-term and promising solution to reduce chemical input in viticulture. However, little is known about the effects of water deficit (WD) on the thiol aromatic potential of new varieties coming up from breeding programs. Varietal thiols such as 3-sulfanylhexan-ol (3SH), 4-methyl-4-sulfanylpentan-2-one (4MSP) and their derivatives are powerful aromatic compounds present in wines coming from odorless precursors in grapes, and could contribute to the wine typicity of such varieties.

Read More