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…

Using δ13C and hydroscapes as a tool for discriminating cultivar specific drought response

Measurement of carbon isotope discrimination in berry juice sugars at maturity (δ13C) provides an integrated assessment of water use efficiency (WUE) during the period of berry ripening, and when collected over multiple seasons can be used as an indication of drought stress response. Berry juice δ13C measurements were carried out on 48 different varieties planted in a common garden experiment in Bordeaux, France from 2014 through 2021 and were paired with midday and predawn leaf water potential measurements on the same vines in a subset of six varieties. The aim was to discriminate a large panel of varieties based on their stomatal behaviour and potentially identify hydraulic traits characterizing drought tolerance by comparing δ13C and hydroscapes (the visualisation of plant stomatal behaviour as a response to predawn water potential). Cluster analysis found that δ13C values are likely affected by the differing phenology of each variety, resulting in berry ripening of different varieties taking place under different stress conditions within the same year. We accounted for these phenological differences and found that cluster analysis based on specific δ13C metrics created a classification of varieties that corresponds well to our current empirical understanding of their relative drought tolerances. In addition, we analysed the water potential regulation of the subset of six varieties (using the hydroscape approach) and found that it was well correlated with some δ13C metrics. Surprisingly, a variety’s water potential regulation (specifically its minimum critical leaf water potential under water deficit) was strongly correlated to δ13C values under well-watered conditions, suggesting that base WUE may have a stronger impact on drought tolerance than WUE under water deficit. These results give strong insights on the innate WUE of a very large panel of varieties and suggest that studies of drought tolerance should include traits expressed under non-limiting conditions.

Aroma profile evaluation in whole grape juices

Table grapes (Vitis labrusca and hybrids) are widely cultivated in Brazil [1] due to the climate, their resistance to disease and the way they are consumed and commercialized, either in-natura or for processing, producing whole juices, jams and table wines.

On sample preparation methods for fermentative beverage VOCs profiling by GCxGC-TOFMS

Study the influence of sample preparation methods on the volatile organic compounds (VOCs) profiling for fermentative beverages by GCxGC-TOFMS analysis. METHODS: Five common sample preparation methods were tested on pooled red wine, white wine, cider, and beer. Studied methods were DHS, Liquid-liquid extraction, mSBSE, SPE and SPME. VOCs were analyzed by GCxGC-TOFMS followed by data analysis with ChromaTOF. RESULTS: The volatile organic compounds (VOCs) profiling results were very dependent on the sample preparation methods.

The legal concept of “cultural heritage” to refurbish the wine sector’s priorities

Following the latest oiv global report (april 26, 2024), the prevailing perception of wine consumption finds itself undergoing one of its most challenging adjustments. It’s plausible to anticipate a shift in the scope of pdo wines towards more human-centered products (wells and stiefel, 2019), necessitating the entire sector to adapt strategies to public interest patterns (touzeau, 2010: 17-31). Previously, a dominant notion of cultural property underscored the value of wine regions; the primary interest revolved around estate owners and retailers, along with vigneron tales.

Generation of radicals in wine by cavitation and study of their interaction with metals, phenols and carboxylic acids

High-power ultrasounds have been related to an accelerated aging of wines, an effect that has been associated to the formation of radical species caused by the cavitation phenomenon [1]. This phenomenon consists of the formation of bubbles in the liquid medium that, when they collapse, cause high-pressure hot spots and temperatures of up to 4800 k [2], notably increasing the reactivity in the medium.