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 winemaking processes on wine polysaccharides, improving by qNMR

Today the knowledge in terms of molecular composition of the colloidal matrix is ​​not enough in order to control its stability, according to the number of winemaking and wine stabilization processes. The physico-chemical processes during the winemaking change the composition and quantity of wine macromolecules. The goal today is to determine which analytical techniques will allow to discriminate these winemaking processes in order to better understand their impact on colloidal matrix stability as well as which molecules are responsible for its instabilities. METHODS: Wines obtained after conventional winemaking were subjected to different fining and chemical stabilization treatments. Different methods were used to investigate the wine macromolecular composition and stability after chemical stabilization, including quantitative and qualitative analyzes of total soluble polysaccharides by extraction under acidified ethanol, and by size exclusion separation as well as qNMR metabolomics. RESULTS: Observation of a slight difference at the quantitative level using classical analysis between the winemaking processes was observed as well as a strong discrimination by qNMR metabolomics.

Methyl Jasmonate Versus Nano-Methyl Jasmonate: Effect On The Stilbene Content In Monastrell Variety

Stilbenes, a kind of non-flavonoid phenolic compounds, have been reported to be responsible for various beneficial effects. Their biological properties include antibacterial and antifungal effects, as well as cardioprotective, neuroprotective and anticancer actions (Guerrero et al. 2009).Several strategies can be used to increase stilbene content in grapes and one of them could be the use of elicitors such as methyl jasmonate. The use of this elicitor has been proven to be efficient in the production of secondary metabolites which increases the quality of wines, but its use also has some drawbacks such as its low water solubility, high volatility, and its expensive cost (Gil-Muñoz et al. 2021).

Assyrtiko wines of Santorini produced by different autochthonous yeasts: Differences in aromatic and organoleptic profiles

Different yeasts were isolated from spontaneous fermentation of Assyrtiko grape must in Santorini Island, Greece. Molecular typing revealed the presence of three Saccharomyces cerevisiae strains (S9, S13, S24) and one strain of the yeast species Nakazawaea ishiwadae (N.i). The four isolated strains were further tested in laboratory scale fermentations of Assyrtiko must in pure inoculation cultures and in sequential inoculation (72 hours) of each S. cerevisiae strain with the strain of N. ishiwadae. All fermentation trials were realised in duplicate.

Harnessing biodiversity to improve grapevine rootstock adaptation to drought

Drought is one of the most challenging threats for viticulture because of its impact on reducing yield and on the composition of grapes.

WINE WITHOUT ADDED SO₂: OXYGEN IMPACT AND EVOLUTION ON THE POLYPHENOLIC COMPOSITION DURING RED WINE AGING

SO₂ play a major role in the stability and wine during storage. Nowadays, the reduction of chemical input during red winemaking and especially the removing SO₂ is a growing expectation from the consumers. Winemaking without SO₂ is a big challenge for the winemakers since the lack of SO₂ affects directly the wine chemical evolution such as the phenolic compounds as well as its microbiological stability.