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…

Effects of different organic amendments on soil, vine, grape and wine, in a long-term field experiment in Chinon vineyard (France)

In a long-term experiment carried out in Chinon vineyard (37, France) during 23 years, the effects of several organic amendments were studied on soil, vine, grapes and wine. Four main treatments were compared on a calcareous sandy soil: control without organic amendment, dry crushed pruning wood at 2.1.t-1.ha-1.year-1 (D1), cow manure at 10 t-1. ha-1.year-1 (D1) and cow manure applied at 20 t-1.ha-1.year-1 (D2). D1 levels were calculated to fill the annual humus losses by mineralization.

Read More

A survey on the rotundone content of 18 grape varieties sourced from a germplasm 

Rotundone, the pepper aroma compound, has been detected in wines made from a large number of grape varieties. However, given the fact that analyzed wines were sourced from different winegrowing regions and seasons, made using different winemaking techniques and at different scales, it remains difficult to assess the real variety potential to produce rotundone.

Read More

Characterization of intact glycoside aroma precursors of recovered minority Spanish red grape varieties by High-Resolution Mass Spectrometry

In Spain, the wide diversity of red grapevine varieties represents an advantage when choosing the most suitable one for cultivation based on different climatic conditions, without implying a loss of their enological potential.

Read More

Photo-oxidative stress and light-struck defect in Corvina rosé wines: influence of yeast nutritional strategies

Light exposure is one of the major factors affecting the sensory quality of rosé wines and resulting in the light-struck fault.

Read More

Nitrogen uptake, translocation and YAN in berries upon water deficit in grapevines with contrasting stomatal sensitivity

Nitrogen (N2) is critical in grape berries, especially in organic wine making. After intake, N2 follows various metabolic and allocation routes and, from veraison, partly reallocates into berries. Water deficit affects the N2 nutrition due to a poor diffusion in soil solution and vascular mobilisation. Also, affects photosynthesis and the energy needed for metabolism, whose extent would depend on the stomatal sensitivity of the plant. We have assessed the effect of a moderate water deficit from pea size, in 3 years old field grown potted plants of Chardonnay (CH) and Cabernet Sauvignon (CS), differing in stomatal sensitivity, on the N2 status of plant parts. Water deficit reduced photosynthesis, leaf area and fresh and dry plant mass along the season, but up to a higher extent in CS.

Read More