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…

EFFECT OF FERMENTATION TEMPERATURE GRADIENT AND SKIN CONTACT ON ESTER AND THIOL PRODUCTION AND TROPICAL FRUIT PERCEPTION IN CHARDONNAY WINES

Wines with tropical fruit aromas have become increasingly more available1,2. With increased availability of different wine styles, it has become important to understand the compounds that cause the fruity aromas in wine. Previous work using micro fermentations showed that fermentation temperature gradients and time on skins resulted in an increase in thiol and ester compounds post fermentation and these compounds are known to cause tropical fruit aroma in wines³. This work aimed to scale up these fermentations/operations to determine if the desired aromas could still be achieved and if there is a perceivable difference in tropical fruit aromas, liking, and emotional response in the wines at the consumer level.

Juvenile-to-adult vegetative phase transition in grapevine 

The sequential activity of miR156 and miR172 controls the juvenile to adult phase transition in many plant species, where miR156 abundance decreases while miR172 increases along plant development. Very little is known about phase transition in horticultural woody species, which show substantially long vegetative phases. In grapevine, phase transition seems to be dissociated, displaying a first transition from juvenile to adult vegetative state in the first year, coincident with tendril differentiation and a subsequent induction of inflorescences in place of some of tendrils in later years under flowering inductive environmental conditions. Since grapevine is a highly heterozygous species, the generation of genetically homogeneous material for replicated transcriptomic analyses from seed-derived plants was a main challenge.

Vineyard microclimate alterations induced by black mulch through transcriptome reshaped the flavoromics of Cabernet Sauvignon

To alter the vineyard microclimate and produce quality wine under a semi-arid climate, black geotextile inter-row mulch (M) was applied for two vintages (2016-2017). The grapes were sampled at three growing stages to conduct the untargeted metabolome and transcriptome analysis. The upregulated genes related to photosynthesis and heat shock proteins confirmed that M weakened the total light exposure and grapes suffered severe heat stress, resulting in lower sugar and higher acids at harvest. The integration of metabolome and transcriptome analysis identified the key genes responsible for the enhancements in phenylalanine, glutamine, ornithine, arginine, and C6 alcohol concentrations, and the downward trend in ε-viniferin, anthocyanins, flavonols, terpenes and norisoprenoids concentrations in M grapes.

Learning from remote sensing data: a case study in the Trentino region 

Recent developments in satellite technology have yielded a substantial volume of data, providing a foundation for various machine learning approaches. These applications, utilizing extensive datasets, offer valuable insights into Earth’s conditions. Examples include climate change analysis, risk and damage assessment, water quality evaluation, and crop monitoring. Our study focuses on exploiting satellite thermal and multispectral imaging, and vegetation indexes, such as NDVI, in conjunction with ground truth information about soil type, land usage (forest, urban, crop cultivation), and irrigation water sources in the Trentino region in North-East of Italy.

Comparison of genotype x environment interaction of clonal and polyclonal grapevine selected materials

Conserving and exploring the intra-varietal diversity of ancient varieties is essential to foster their use in the future, preserving the traditions and history of ancient growing regions and their wines. The conservation of representative samples of ancient varieties and the utilization of intra-varietal variability through polyclonal selection are advisable strategies to save and promote the cultivation of each variety, respectively.