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…

The regulation of ABA-induced anthocyanin accumulation in grape berry

Color is a key quality trait for grape berry and the producing wines. Berry color of red genotypes is mainly determined by the quantity and composition of anthocyanins accumulated in the skin and/or pulp. Both genetic and environmental factors could influence the quantity and composition of anthocyanins, while the underlying mechanisms are not fully clear. To explore the mechanisms underlying the diversity of anthocyanin accumulation in grape berry, we compared two grapevine genotypes showing distinct sensitivities to ABA-induced anthocyanin biosynthesis, where one genotype showed minor responses to exogenous ABA application while the other showed significant increase in anthocyanins after exogenous ABA application.

La Région Délimitée du Douro et le Vin de Porto — un terroir historique —

The viticulture of the Douro Delimited Region, one of the heirs of ancestral viticulture, traditionally empirical and of quality, while integrating modernity and contemporary tools, respects and has always present the principles on which it was developed.

The use of viticultural and oenological performance of grapevines to identify terroirs: the example of Sauvignon blanc in Stellenbosch

Identification and characterisation of terroirs depends on knowledge of environmental parameters, functioning of the grapevine and characteristics of the final product. A network of plots of Sauvignon blanc was delimited in commercial vineyards in proximity to weather stations at 20 localities and their viticultural and oenological response was monitored for a period of seven years. These experimental plots were further characterised with respect to climate, soil and topography.

Upscaling the integrated terroir zoning through digital soil mapping: a case study in the Designation of Origin Campo de Borja

homogeneous zones by intersecting several partial zonings of major factors that influence vineyard growth. Each of them follows specific process from their corresponding disciplines. Soil zoning specifically refers to a Soil Resource Inventory map that has traditionally been generated by conventional soil mapping methods. These methods have shortcomings in reaching fine cartographic and categorical details and involve significant expenses, which undermines their applicability. A new framework named Digital Soil Mapping has introduced quantitative models by statistical techniques to establish soil-landscape relationships and is able to provide intensive scale cartography.

In the present study, a microzoning at 1:10.000 scale is generated from an initial zoning, where the conventional soil map with polytaxic map units is replaced by a new one from digital techniques that disaggregates them. The comparison between the zonings considers a quantitative evaluation of capability for each Homogeneous Terroir Unit by means of the Viticultural Quality Index and its categorization based on its distribution by map. The spatial intersection of both maps gives rise to a confusion matrix in which the flows of class variations after the substitution are assessed.

The results show a five-fold increase in the number of Homogeneous Terroir Units identified and a larger differentiation among them, evidenced by a wider range in the capability index distribution. Both elements are accompanied by an increase in the detection of areas of higher potential within previously undervalued uniform zones.These features are a direct effect of the improvements brought by Digital Soil Mapping techniques and would verify the advantages of their implementation in the Integrated Terroir zoning. Eventually, such new highly detailed terroir units would benefit precision viticulture and sustainable management practices.

Adaptation of Lactobacilli towards low ph and SO2 to develop MLF in base musts for sparkling wines

In some white wines, malolactic fermentation (MLF) is very interesting, and for low pH wines this process is particularly difficult. Although MLF is generally not recommended for sparkling white wine, some winemakers prefer to promote MLF to contribute to organoleptic complexity. Oenococcus oeni is generally the bacterium of choice for MLF.