terclim by ICS banner
IVES 9 IVES Conference Series 9 Haplotype-Resolved genome assembly of the Microvine

Haplotype-Resolved genome assembly of the Microvine

Abstract

Developing a tractable genetic engineering and gene editing system is an essential tool for grapevine. We initiated a plant transformation and biotechnology program at Oregon State University using the grape microvine system (V. vinifera) in 2018 to interrogate gene-to-trait relationships using traditional genetic engineering and gene editing. The microvine model is also used for nanomaterial-assisted RNP, DNA, and RNA delivery. Most reference genomes and annotations for grapevine are collapsed assemblies of homologous chromosomes and do not represent the specific microvine cultivar ‘043023V004’ under study at our institution. We used a trio-binning method combining PacBio HiFi and parental Illumina reads to develop a high-quality, haplotype-resolved microvine genome. This genome was refined using chromosome scaffolding with high-throughput chromosome conformation capture (Hi-C). To evaluate genome quality, we compared this genome with our own highly curated microvine genome, which was produced using a combination of Oxford Nanopore and PacBio Sequel I sequencing. While the new genome retains considerable large-scale structural synteny with existing grape genomes, it also revealed significant differences between haplotypes. The phasing approach has elucidated the unique allelic contributions of essential gene families like GRAS, which contribute to the microvine dwarfing, or MYB, involved in regulating pigment accumulation in berries. The roles of additional gene variants, alongside associated alternative-splicing events, provide insights into the dynamic regulation of these key gene families across haplotypes. This comprehensive genomic resource will accelerate the functional characterization of complex molecular gene interactions, enhance molecular marker development, and improve the precision of genome editing tools in grapevine research.

Download the abstract

DOI:

Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Poster

Authors

Samuel Talbot1*, Steven Carrell2, Brent Kronmiller2, Satyanarayana Gouthu1, Luca Bianco3, Paolo Fontana3, Mickael Malnoy3, and Laurent G. Deluc1&4

1Department of Horticulture, Oregon State University, Corvallis, USA
2Center for Quantitative Life Sciences, Oregon State University, Corvallis, USA,
3Foundation Edmund Mach, San Michelle All’addige, Italy
4Oregon Wine Research Institute, Oregon State University, Corvallis, USA

Contact the author*

Keywords

Microvine, HiFi, Haplotype-resolved genome, trio-binning method

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

Aroma and quality assessment for vertical vintages using machine learning modelling based on weather and management information

Wine quality traits are usually given by parameters such as aroma profile, total acidity, alcohol content, colour and phenolic content, among others

Read More

SHIRAZ FLAVONOID EXTRACTABILITY IMPACTED BY HIGH AND EXTREME HIGH TEMPERATURES

Climate change is leading to an increase in average temperature and in the severity and occurrence of heatwaves, and is already disrupting grapevine phenology. In Australia, with the evolution of the weather of grape growing regions that are already warm and hot, berry composition including flavonoids, for which biosynthesis depends on bunch microclimate, are expected to be impacted [1]. These compounds, such as anthocyanins and tannins, contribute substantially to grape and wine quality. The goal of this research was to determine how flavonoid extraction is impacted when bunches are exposed to high (>35 °C) and extreme high (>45 °C) temperatures during berry development and maturity.

Read More

CropManage online decision support tool for irrigation scheduling of vineyards

CropManage (CM) is an online decision support service (DSS) developed by the University of California, Division of Agriculture and Natural Resources for assisting farmers with efficiently managing water and nitrogen fertilizer to match the site-specific needs of their crops.

Read More

Detection of spider mite using artificial intelligence in digital viticulture

Aim: Pests have a high impact on yield and grape quality in viticulture. An objective and rapid detection of pests under field conditions is needed. New sensing technologies and artificial intelligence could be used for pests detection in digital viticulture. The aim of this work was to apply computer vision and deep learning techniques for automatic detection of spider mite symptoms in grapevine under field conditions. 

Read More

Insights into the stable isotope ratio variability of hybrid grape varieties

The wine industry faces the consumer’s increasing demand for a sustainable and environmentally-friendly production [1]. This demand has been shared and boosted by the European Union within the European Green Deal in the Farm to Fork strategy that aims to reduce a 50% the pesticide utilisation in farming systems. Among the agronomical approaches so far proposed, the use of mould resitant hybrid varieties -based on crossings of Vitis vinifera with other Vitis spp [2]- with a high tolerance to the attack of vine patogens is gaining the vinegrowers attention and the production area is continuously increasing

Read More