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…

Nitrogen uptake, translocation and YAN in berries upon water deficit in grapevines with contrasting stomatal sensitivity

Nitrogen (N2) is critical in grape berries, especially in organic wine making. After intake, N2 follows various metabolic and allocation routes and, from veraison, partly reallocates into berries. Water deficit affects the N2 nutrition due to a poor diffusion in soil solution and vascular mobilisation. Also, affects photosynthesis and the energy needed for metabolism, whose extent would depend on the stomatal sensitivity of the plant. We have assessed the effect of a moderate water deficit from pea size, in 3 years old field grown potted plants of Chardonnay (CH) and Cabernet Sauvignon (CS), differing in stomatal sensitivity, on the N2 status of plant parts. Water deficit reduced photosynthesis, leaf area and fresh and dry plant mass along the season, but up to a higher extent in CS.

An operational model for capturing grape ripening dynamics to support harvest decisions

Grape ripening is a critical phenophase during which many metabolites driving wine quality are accumulated in berries. Major changes in berry composition include a rapid increase in sugar and a decrease in malic acid content and concentration. Its duration is highly variable depending on grapevine variety, climatic parameters, soil type and management practices.

Relation between phenolic content, antioxidant capacity, oxygen consumption rate of diverse tannins

The work was aimed at comparing some analytical methods used to characterize oenological tannins and the measure of oxygen consumption rate (OCR), in order to provide oenologists with a rapid method to test the antioxidant capacity of tannin based products and a tool to choose the best suited product for each purpose.

Management of cover plants impacted the composition of Cabernet Sauvignon red wines in a temperate region of Brazil

– Several practices can be applied to vineyards in order to ensure good healthy for grapevines, adequate yield and fruit quality. Among them, the use of cover crops is a relevant option for soil management. It increases the organic matter, improves water infiltration, reduces risks of soil erosion and greenhouse gas emissions, in addition improving biodiversity in the vineyard.

Health space in vine spa in the world

This elaboration presents vine spa has precious contribution of social development health and well being in culture of wine regions. The majority of the vine-spas in the world draw raw materials from the vineyard; both for cosmetics treatments and for dishes in their restaurants. Vitis vinifera vine provides fresh grapes for dishes and massages, seeds and oil from the seeds, as well as the leaves, and its extracts, and above all the wine.