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…

Spatio-temporal analysis of grapevine water behaviour in hillslope vineyards. the example of corton hill, Burgundy

Hillslope vineyards show various and complex water dynamics between soil and plants, and in order to gain further insight into this phenomenon, 8 grapevine plots were monitored during three vintages, from 2010 to 2013, on Corton Hill, Burgundy, France.

Read More

Cultures des vignobles en forte pente: possibilités de mécanisation. Effet de l’exposition et de l’orientation des rangs

Plus de la moitié du vignoble suisse (14’000 ha) est situé sur des coteaux en forte pente (> 30%). Dans certains vignobles, la pente naturelle du terrain a été réduite par la construction de terrasses soutenues par des murs.

Read More

Study of the “Charentes terroir” for wine production of Merlot and Sauvignon: method, installation of the experimental device, first results

Cognac vineyard is mainly dedicated to brandy production. Within the vineyard restructuring context, one part is turned over wine varieties for wine production (about 1,500 ha planted from 1999 to 2005). Today, the new wine producers need technical references about qualitative potential of the « Charentes Terroir », varieties and adapted vineyard management.
In order to answer to this professional request, an observatory of 18 plots of Merlot and 12 plots of Sauvignon have been laid out since 2003 and 2004 on various kinds of pedoclimate.

Read More

A comprehensive ecological study of grapevine sensitivity to temperature; how terroir will shift under climate change

Fossil fuel combustion continues to drive increases in atmospheric carbon dioxide, consequently elevating the global annual mean temperature and specifically increasing the growing season temperatures in many of the world’s most important wine growing regions (IPCC 2014; Jones et al 2005). Grapes are sensitive to changes in growing season temperatures, and past models have shown a direct link between warming temperatures and earlier harvest dates (Cook and Wolkovich 2016). Globally, there have been shifts of 1-2 weeks for wine growing regions (Wolkovich et al 2017 and references within). The phenological shifts resulting from growing season temperature increases are documented internationally, and models predicting phenology using temperature are becoming more precise (Parker et al 2011).

Read More

Unveiling the unknow aroma potential of Port wine fortification spirit taking advantage of the comprehensive two-dimensional gas chromatography

Port wine is a fortified wine exclusively produced in the Douro Appellation (Portugal) under very specific conditions resulting from natural and human factors. Its intrinsic aroma characteristics are modulated upon a network of factors, such as the terroir, varieties and winemaking procedures that include a wide set of steps, namely the fortification with grape spirit (ca. 77% v/v ethanol).

Read More