ArticleNature communications2020
Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers, 1 of them a synthesis that pooled it.
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75 citing papers in PubMed, 1 synthesis or guideline pooled it, 154 citations in OpenAlex.
- 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
- Advances in genomics-driven genetic decoding and genomic design breeding in tomato.Horticulture research · 2026Article
- Genomics Approach Links ROS-Scavenging to Enhanced Lateral Root Development Under Salt Stress in Tomato.Plant, cell & environment · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- Chromosome-Scale Haplotype Genome Assemblies for the Australian Mango 'Kensington Pride' and a Wild Relative, Mangifera laurina, Provide Insights Into Anthracnose-Resistance and Volatile Compound Biosynthesis Genes.Plant biotechnology journal · 2026Article
- The Camellia sinensis var. sinensis cv. Fuding Dabaicha genome unveils structural variation-driven metabolic innovation.Nature communications · 2026Article
- Genetic architecture of the tomato fruit lipidome.PNAS nexus · 2026Article
- Structural Variants Contribute to Phenotypic Variation in Maize.Molecular ecology · 2025Article
- The Evolutionary Dynamics of Genetic Mutational Load Throughout Tomato Domestication History.Molecular ecology · 2025Article
- Tomato and its relatives are breaking the genomics barriers.Journal of experimental botany · 2025Review
- Transcriptional control of tomato fruit development and ripening.Journal of experimental botany · 2025Review
- A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus.BMC genomics · 2025Article
- Genetic basis of grain protein and fat contents preliminarily decoded in a foxtail millet biparental recombinant inbred line population.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Co-option of transcription factors drives evolution of quantitative disease resistance against a necrotrophic pathogen.The Plant cell · 2025Article
- Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network.International journal of molecular sciences · 2025Article
- Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.Scientific reports · 2025Article
- Genome of root celery and population genomic analysis reveal the complex breeding history of celery.Plant biotechnology journal · 2025Article
- Transcriptomics in solanaceous crop improvement: advances and opportunities.Frontiers in plant science · 2025Review
- Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing.Nature genetics · 2025Article
- Structural variants contribute to phenotypic variation in maize.bioRxiv : the preprint server for biology · 2024Article
15 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions identifies alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous SVs overlapping genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.
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