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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.

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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

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Keywords

Microvine, HiFi, Haplotype-resolved genome, trio-binning method

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

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