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…

Mean polymerization degree of proanthocyanidins of grape seeds, skins and wines from Agiorgitiko (cv. Vitis vinifera): Differences among vintages

Grape phenolic compounds are very important constituents of red wine because, in addition to their antioxidant properties, they contribute to color, astringency and bitterness, oxidation reactions, interactions with proteins and ageing behavior of wines. The aim of our study was to assess the structural characteristics of grape and wine proanthocyanidins of Agiorgitiko variety and to evaluate the influence of the vintage year. Twelve vineyard locations were designated in the Nemea wine region. For three consecutive years (2012-2014), the grapes were harvested at technological maturity and the method of phloroglucinolysis was employed to determine the mean degree of polymerization (mDP) and subunit composition of the samples.

Impacts of the projected changes in temperature under scenarios of climate change on vine phenology of three red varieties cultivated in Rioja (Spain)

Grapevine is one of the crops that may suffer more negative impacts
under climate change, due not only to changes in temperature but also due to water available. Some of the most direct effects of climate variability on grapevines are the changes in the onset and timing of phenology events and changes in the length of the growing season, which may have further effects on grape quality. The aim of this research was to analyze the changes in vine phenology of some red varieties (Tempranillo, Grenache and Carignan) cultivated in Rioja Oriental (Rioja DOCa), under different climate change scenarios.

Viticulture and climate: from global to local

Aims: This review aims to (1) present the multiple interests of studying and depicting and climate spatial variability for vitivinicultural terroirs study; (2) explain the factors that affect climate spatial variability according to the spatial scale considered and (3) provide guidelines for climate zoning considering challenges linked to each methodology considered.

The invasive seaweed Rugulopteryx okamurae: an innovative plant protective extract

Grapevine downy mildew, caused by Plasmopara viticola, is a devastating disease worldwide. Most commercially important cultivars of the European grapevine are highly susceptible and therefore require the recurrent application of synthetic fungicides to control the disease, copper being the most frequently used. However, with European Union goals to lower their usage, there is a need to develop innovative and sustainable strategies. In this respect, seaweeds have proven to have great potential as phytosanitary agents, in addition to promoting plant growth and stress-tolerance.

Atmospheric modeling: a tool to identify locations best suited for vine cultivation. Preliminary results in the Stellenbosch region

The choice of sites for viticulture depends on natural environmental factors, particularly climate, as grapevines have specific climatic requirements for optimum physiological performance and berry quality achievement. In the Stellenbosch wine-producing region, the complex topography and the proximity of the ocean create a variety of topoclimates resulting in different growth conditions for vines within short distances.