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…

A look back at 20 years of exploring the future of the vines and wines sector

What if, in 25 years, most wines were dealcoholized and flavored ? What if vines were only cultivated to combat erosion, store carbon, and provide anthocyanins…? What if climate change completely changed the list of vine varieties cultivable for wine production in France? What if food stores had completely disappeared in favor of virtual platforms? And if… because the long-term future is not predetermined and therefore not knowable, because the future is open to several possibilities, because the future does not emerge from nothing but from the present which conceals heavy trends and weak signals, prospective approaches make it possible to consider the room for maneuver that actors have to promote the advent of a future, which we can hope to be chosen, at least in part.

HEAT BERRY : Sensitivity of berries ripening to higher temperature and impact on phenolic compounds in wine

The grapevine is an important economical crop that is very sensitive to climate changes and microclimate. The observations made during the last decades at a vineyard scale all concur to show the impact of climate change on vine physiology, resulting in accelerated phenology and earlier harvest (Jones and Davis 2000). It is well-known that berry content is affected by the ambient temperature. While the first experiences were primarily conducted on the impact of temperature on anthocyanin accumulation in the grape, few studies have focused on others component of phenolic metabolism, such as tannins.

Evaluation of consumer behaviour, acceptance and willingness to return of faulty wines

The analysis of consumer attitudes towards wine, especially towards wines perceived as faulty, is an aspect that requires more research than has been carried out so far [1]. This study aims to analyse consumer behaviour in situations involving the consumption of faulty wines and to assess the level of acceptance of such wines.

Diversity of arbuscular mycorrhizal fungi on grapevine roots across an edaphoclimatic gradient

Challenges associated with climate change, such as soil erosion and drought, have impacted viticulture across wine regions globally in recent decades. As winegrowers struggle to maintain yield and quality standards under these conditions, methods to adapt to and mitigate the impacts of climate change have become more prevalent. One potential mitigation strategy is to enhance symbiotic interaction of grapevine roots with arbuscular mycorrhizal fungi (AMF).

Climate change projections in serbian wine-growing regions

Changes in bioclimatic indices in wine-growing region of Serbia are analyzed under the RCP 8.5 IPCC scenario.