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…

Evaluation of aroma characteristics in Vitis amurensis grapes across different regions by using HS-SPME-GC/MS

Background: Aroma compounds are important secondary metabolite in grapes and play important roles in the flavor and quality of grape berries and their wines. Vitis amurensis grape belongs to the East Asian Vitis spp., with excellent cold and disease resistance, and exhibits strong brewing potential. However, it has not been effectively utilized and there is no systematic research on the aroma compounds of V. amurensis grapes.
Methods: To provide sufficient experimental evidence for the characteristic aroma of V. amurensis grape, HS-SPME-GC/MS was used to identify the aroma compounds of five V. amurensis (‘Beiguohong’, ‘Beiguolan’, ‘Shuangfeng’, ‘Shuanghong’, ‘Shuangyou’) and three interspecific hybrids (‘Beibinghong’, ‘Xuelanhong’, ‘Zuoyouhong’) grapes in Zuojia and Ji’an. The grape berries were collected at harvest in 2020, 2021 and 2022.

Influence of processing parameters on aroma profile of conventional and ecological Cabernet-Sauvignon red wine during concentration by reverse osmosis

Wine aroma represents one of the most important quality parameter and it is influenced by various factors (viticulture and vinification techniques, climate or storage conditions etc.). Wines produced from conventionally and ecologically grown grapes of same variety have different chemical composition and aroma profile [1]. Aroma profile of wine can be also influenced by additional treatment of wine, such as concentration of wine by reverse osmosis (RO). Reverse osmosis represents a pressure-driven membrane separation technique that separates the initial wine on the retentate or concentrate that is retained on the membrane, and permeate that passes through it [2]. Wine permeate usually containes water, ethanol, acetic acid and several low molecular weight compounds that can pass through the membrane. This property enables the use of reverse osmosis membranes for wine concentration, partial dealcoholization, acetic acid or aroma correction [3,4].

A multivariate approach using attenuated total reflectance mid-infrared spectroscopy to measure the surface mannoproteins and β-glucans of yeast cell walls during wine fermentations

Yeast cells possess a cell wall comprising primarily glycoproteins, mannans, and glucan polymers. Several yeast phenotypes relevant for fermentation, wine processing, and wine quality are correlated with cell wall properties. To investigate the effect of wine fermentation on cell wall composition, a study was performed using mid-infrared (MIR) spectroscopy coupled with multivariate methods (i.e., PCA and OPLS-DA). A total of 40 yeast strains were evaluated, including Saccharomyces strains (laboratory and industrial) and non-Saccharomyces species. Cells were fermented in both synthetic MS300 and Chardonnay grape must to stationery phase, processed, and scanned in the MIR spectrum.

ASSESSMENT OF ‘DOLCETTO’ GRAPES AND WINES FROM DIFFERENT AREAS OF OVADA DOCG

Dolcetto (Vitis vinifera L.) is one of the traditionally cultivated varieties in Piedmont (north-east Italy). Dolcetto wines have long been associated with local consumption and they are little known internationally. In particular, the Ovada area (south-east Piedmont), even if it represents a small share of the regional PDO Dolcetto production, is one of the oldest and vocated territory, giving wine also suitable for aging. In this study, the basic composition and phenolic content of Dolcetto grapes for Ovada DOCG wines have been investigated in three different vintages (2020-2022), as well as the main aspects of the derived commercial and experimental wines (basic parameters, phenolics, volatile compounds, sensory properties).

Improved vineyard sampling efficiency using aerial NDVI

Random sampling is often considered to be the best protocol for fruit sampling because it is assumed to produce a sample that best represents the vineyard population.