ArticleCell2020
Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.
Article in Cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 461 papers.
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Who cites it
461 citing papers in PubMed.
- Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges.Molecular biology and evolution · 2026Article
- Comparative evaluation of GWAS-prioritized SNP, SSR, and insertion-type structural variant marker panels for genomic prediction in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Review
- Transposable Element Dynamics Drive the Genomic Evolution and Phenotypic Diversification of Allotetraploid Common Carp.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Pan-genome characterization of the maize 4CL gene family and its dynamic responses to abiotic stress.Plant molecular biology · 2026Article
- Multi-variant GWAS and genomic prediction dissect the genetic architecture underlying tomato fruit weight.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Haplotype-resolved regulation of secondary metabolism in cannabis.Horticulture research · 2026Article
- Advances in genomics-driven genetic decoding and genomic design breeding in tomato.Horticulture research · 2026Article
- Deep Learning for Deciphering the Plant Cis-Regulatory Code.Plants (Basel, Switzerland) · 2026Review
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- Integrated Analysis of SNPs and Structural Variations via High-depth Whole-genome Sequencing Reveals the Genetic Architecture and Optimizes Genomic Prediction in Chickens.Poultry science · 2026Article
- Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.Nature genetics · 2026Article
- A transposable element-derived regulatory variation inHorticulture research · 2026Article
- Fine-tuning quantitative agronomic traits by manipulating gene copy number in rice.The New phytologist · 2026Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- New biologically relevant resistance to bacterial wilt in heat-stressed tomato revealed by two-reference Genome Wide Association.PLoS genetics · 2026Article
- Genome Wide Structural Variants Provide Insights Into Population Structure and Genetic Divergence in Pacific White Shrimp (Evolutionary applications · 2026Article
- Telomere-to-telomere genome assembly of pumpkin (Horticulture research · 2026Article
- Article
401 more citing papers are in PubMed but not listed here.
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35 authors.
Funding
Abstract
Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.
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