The population genetics of structural variants in grapevine domestication
Open accessPublished version of a preprint
Abstract
Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their evolutionary genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution.
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High hemizygosity has been reported in the genomes of clonally propagated grapevine.
“High hemizygosity has been reported in the genomes of clonally propagated grapevine (Zhou et al., 2019), suggesting that this type of SV might be common in plants and could contribute to RI.”
From Genomics of plant speciation (2023) · cites this paper as Zhou et al., 2019
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“High hemizygosity has been reported in the genomes of clonally propagated grapevine (Zhou et al., 2019), suggesting that this type of SV might be common in plants and could contribute to RI.”
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- Authors
- Zhou, Y., Minio, A., Massonnet, M., Solares, E., Lv, Y., Beridze, T., Cantu, D., & Gaut, B. S.
- Affiliations
- University of California, Irvine (US)
- University of California, Davis (US)
- Agricultural University of Georgia (GE)
- Corresponding author
- Gaut, Brandon S.
- ORCID
- Venue
- Nature Plants
- Published
- 2019-09-09
- Volume
- 5
- Issue
- 9
- Pages
- 965-979
- ISSN
- 2055-026X (ISSN-L)
- 2055-0278
- OpenAlex
- W2972606315
- Cited by
- 339
- References
- 9
- Citations by year
- 2026: 31 · 2025: 49 · 2024: 36 · 2023: 48 · 2022: 48 · 2021: 70 · 2020: 43 · 2019: 13
- FWCI
- 34.66
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Plants (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, cc-by)
- Funders
- National Science Foundation (1741627)
- Lohr and Martini are companies who support the laboratory of D. Cantu but have no conflicting interest
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Horticultural and Viticultural Research
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- structural variants, grapevine domestication, grapevine, Chardonnay, Cabernet Sauvignon, purifying selection, chromosomal inversions, translocation, clonal propagation, hemizygosity, genomic divergence, sex determination region, population genetics
- MeSH terms
- Domestication, Phenotype, Genome, Plant, Vitis, Genomic Structural Variation
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