ArticleNature genetics2019
The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor.
Article in Nature genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 348 papers, 3 of them syntheses that pooled it.
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Who cites it
348 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- eQTL Meta-Analysis Reveals Conserved and Population-Specific Regulatory Variation Underlying Nutritional Trait Evolution and Domestication in Tomato.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Pooled it
- Advancing crop improvement through GWAS and beyond in mung bean.Frontiers in plant science · 2024Pooled it
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
- Reactivation of a loss-of-function SlGLK2 allele by frame-restoring genome editing in tomato.Plant cell reports · 2026Article
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- Graph-based pangenomics reveals the genetic basis of agronomic traits in tomato fruits.Horticulture research · 2026Article
- Advances in genomics-driven genetic decoding and genomic design breeding in tomato.Horticulture research · 2026Article
- QTL Mapping for Leaf Rust Resistance in a Wheat Recombinant Inbred Line Population of Liang66-S/Hengmai28.Plants (Basel, Switzerland) · 2026Article
- Pan-Genomic Dissection of GH1 β-Glucosidases inPlants (Basel, Switzerland) · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Genomic Sampling and Population Structure of Farmer-Maintained Varieties Reveal Previously Uncharacterized Diversity of Theobroma cacao L. in Costa Rica.Molecular ecology · 2026Article
- Article
- KCFtools: rapid alignment-free method for introgression screening and GWAS using k-mer profiles.Bioinformatics (Oxford, England) · 2026Article
- The Pan-Genome of 1107 Spotted Sea Bass Accessions Reveals Gene Evolution Patterns During Domestication Selection.Molecular ecology resources · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Mammalian growth factors enhance regeneration in transgenic tomato lines.Transgenic research · 2026Article
- From Genetic Diversity to Genetic Gain: Molecular Approaches and Breeding Strategies in Tomato with Insights from Lithuanian Germplasm.International journal of molecular sciences · 2026Review
- A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution.Plant biotechnology journal · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
288 more citing papers are in PubMed but not listed here.
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21 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in the TomLoxC promoter selected against during domestication. Quantitative trait locus mapping and analysis of transgenic plants reveal a role for TomLoxC in apocarotenoid production, which contributes to desirable tomato flavor. In orange-stage fruit, accessions harboring both the rare and common TomLoxC alleles (heterozygotes) have higher TomLoxC expression than those homozygous for either and are resurgent in modern tomatoes. The tomato pan-genome adds depth and completeness to the reference genome, and is useful for future biological discovery and breeding.
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