ArticleNature plants2019
The population genetics of structural variants in grapevine domestication.
Article in Nature plants, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 177 papers.
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177 citing papers in PubMed.
- Unlocking the future of crop improvement with crop wild relatives.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Dissecting the genetic basis of climatic adaptation in wild relatives (Malus baccata) for climate-resilient apple breeding.Journal of integrative plant biology · 2026Article
- Automated Seed Morphometry Identifies Morphotypes Associated with Major Grapevine Haplotypic Lineages.Plants (Basel, Switzerland) · 2026Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- Analysis of deep-resequencing data of 984 soybean accessions reveals structural variations underlying agronomic traits.Nature communications · 2026Article
- A dual genome-methylome map of clonal evolution in grapevine.Genome biology · 2026Article
- Haplotype-Resolved 3D Genomic Landscapes and Their Impacts on Agronomic Traits in Grapevine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Haplotype-resolved T2T genome and population resequencing provide insights into the domestication and mogroside biosynthesis ofHorticulture research · 2026Article
- Haplotype-resolved genome of 'Pinot Noir' reveals DNA polymorphisms and allele-specific expression shaping terroir adaptation.Molecular horticulture · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Ancient DNA reveals 4000 years of grapevine diversity, viticulture and clonal propagation in France.Nature communications · 2026Article
- Graph-based pangenome reveals structural variation dynamics during cucumber breeding.Nature genetics · 2026Article
- Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape.Nature communications · 2026Article
- Sub-pangenome analysis reveals structural variants associated with fruit color and bacterial wilt resistance in eggplant.Nature communications · 2026Article
- A complex reciprocal translocation is linked to reduced gamete viability in a loose-bunch grapevine somatic variant.BMC plant biology · 2026Article
- The Camellia sinensis var. sinensis cv. Fuding Dabaicha genome unveils structural variation-driven metabolic innovation.Nature communications · 2026Article
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- Chromosome-level genome assembly of Hamlin sweet orange and transcriptomic insights into MADS-box gene regulation of secondary fruit development.Frontiers in plant science · 2026Article
- Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in China.Horticulture research · 2026Article
- Pangenome analyses of tea plants reveal structural variations driving gene expression alterations and agronomic trait diversification.Nature communications · 2025Article
117 more citing papers are in PubMed but not listed here.
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8 authors.
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No grant is acknowledged in the PubMed record.
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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