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…

Potential of native Uruguayan yeast strains for production of Tannat wine

Must fermentation is a complex process influenced by various factors, especially microbiological activities. The characteristics and quality of the resulting wine are closely linked to the stages that unfold throughout this progression.

Use of satellite in precision viticulture: the Franciacorta experience

Today, the concept of precision vine management (or site-specific viticulture) has a great relevance. It is based on the practice of a different management in relation to the different features of the crop site. In this way, all practices should be adapted to the land spatial variability and should be linked to the real needs of vines.

Sensory profiles and European Consumer Preference related to Aroma and Phenolic Composition of Wines made from Fungus Resistant Grape Varieties

New grape varieties with several resistance loci towards powdery and downy mildew allows to significantly reduce the use of fungicides

Use of pectinolytic yeast in wine fermentations

The use of pectinolytic enzymes in winemaking is state of the art. These enzymes catalyse the degradation of pectic substances through depolymerization (hydrolases and lyases) and de-esterification. As a result, it supports the extraction of juice and facilitates filtration. It has also been shown in winemaking that the presence of pectinolytic enzymes improves the stability, taste, texture, colour and aroma of products. With regard to enzymes currently applied in winemaking, enzymes derived from filamentous fungi dominate the enzyme industry. Fungal-based pectinolytic enzymes specifically require purification from the culture medium to eliminate unwanted side reactions, which is poorly sustainable. Some non-traditional yeast strains have been reported to exhibit pectinolytic activities. Therefore, the direct use of pectinolytic yeast during wine fermentation process can be an attractive and alternative source for the use of enzymes as input.

Modelling vine water stress during a critical period and potential yield reduction rate in European wine regions: a retrospective analysis

Most European vineyards are managed under rainfed conditions, where seasonal water deficit has become increasingly important. The flowering-veraison phenophase represents an important period for vine response to water stress, which is seldomly thoroughly evaluated. Therefore, we aim to quantify the flowering-veraison water stress levels using Crop Water Stress Indicator (CWSI) over 1986–2015 for important European wine regions, and to assess the respective potential Yield Lose Rate (YLR). Additionally, we also investigate whether an advanced flowering-veraison phase may help alleviating the water stress with improved yield. A process-based grapevine model STICS is employed, which has been extensively calibrated for flowering and veraison stages using observed data at 38 locations with 10 different grapevine varieties. Subsequently, the model is being implemented at the regional level, considering site-specific calibration results and gridded climate and soil datasets. The findings suggest wine regions with stronger flowering-veraison CWSI tend to have higher potential YLR. However, contrasting patterns are found between wine regions in France-Germany-Luxembourg and Italy-Portugal-Spain. The former tends to have slight-to-moderate drought conditions (CWSI<0.5) and a negligible-to-moderate YLR (<30%), whereas the latter possesses severe-to-extreme CWSI (>0.5) and substantial YLR (>40%). Wine regions prone to a high drought risk (CWSI>0.75) are also identified, which are concentrated in southern Mediterranean Europe. An advanced flowering-veraison phase may have benefited from cooler temperatures and a higher fraction of spring precipitation in wine regions of Italy-Portugal-Spain, resulting in alleviated CWSI and moderate reductions of YLR. For those of France-Germany-Luxembourg, this can have reduced flowering-veraison precipitation, but prevalent alleviations of YLR are also found, possibly because of shifted phase towards a cooler growing season with reduced evaporative demands. Overall, such a retrospective analysis might provide new insights towards better management of seasonal water deficit for conventionally vulnerable Mediterranean wine regions, but also for relatively cooler and wetter Central European regions.