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.

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…

Impact of monopolar and bipolar pulsed electric fields on the quality of Tinta Roriz wines

Pulsed electric fields (pef) technology holds significant promise for the agrifood industry, considering the capacity of inducing cell electroporation, due to the disruption of cellular membranes. Pef-induced permeabilization is dependent of the chosen treatment protocol (i.e. Pulse shape, electrical field strength, specific energy) and of the matrix’s characteristics (i.e. Cell radii and size, ph, electrical conductivity).

From bush to glass: unlocking the potential of indigenous microbes in Australian wines

Global trends in the wine industry are changing, which is caused by consumer demands for aroma and flavour innovation. Producers in Australia, the sixth globally ranked wine producing country, are embracing this trend by exploring non-conventional yeast species to improve sensory qualities and achieve fermentation advantages.

Mapping and tracking canopy size with VitiCanopy

Understanding vineyard variability to target management strategies, apply inputs efficiently and deliver consistent grape quality to the winery is essential. However, despite inherent vineyard variability, the majority are managed as if they are uniform. VitiCanopy is a simple, grower-friendly tool for precision/digital viticulture that allows users to collect and interpret objective spatial information about vineyard performance. After four years of field and market research, an upgraded VitiCanopy has been created to achieve a more streamlined, technology-assisted vine monitoring tool that provides users with a set of superior new features, which could significantly improve the way users monitor their grapevines. These new features include:
• New user interface
• User authentication
• Batch analysis of multiple images
• Ease the learning curve through enhanced help features
• Reporting via the creation of colour maps that will allow users to assess the spatial differences in canopies within a vineyard.
Use-case examples are presented to demonstrate the quantification and mapping of vineyard variability through objective canopy measurements, ground-truthing of remotely sensed measurements, monitoring of crop conditions, implementation of disease and water management decisions as well as creating a history of each site to forecast quality. This intelligent tool allows users to manage grapevines and make informed management choices to achieve the desired production targets and remain profitable.

Phenolic compounds present in natural haze protein of Sauvignon white wine

The aim of this work was the identification and quantification of polyphenols present in natural precipitate of a Sauvignon wine. Phenol analysis in wine precipitate was based on acid hydrolysis, CG- MS after derivatization, and LC-MS.

Investigation on the potentiality of a biostimulant by Fabaceae tissues and rich in triacontanol to enhance grapevine resilience under drought stress

The primary objective of this research was to investigate the potential benefits of a Fabaceae-based product rich in triacontanol (a long-chain alcohol) applied to Vitis vinifera cv. Merlot, on key physiological and productive parameters of grapevines under controlled water stress conditions.