ArticleBMC genomics2015
Genomic variation in tomato, from wild ancestors to contemporary breeding accessions.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers, 1 of them a synthesis that pooled it.
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Who cites it
106 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor.Nature communications · 2019Pooled it
- Multi-variant GWAS and genomic prediction dissect the genetic architecture underlying tomato fruit weight.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- New biologically relevant resistance to bacterial wilt in heat-stressed tomato revealed by two-reference Genome Wide Association.PLoS genetics · 2026Article
- Review
- Metabolic and Biochemical Responses of Heirloom and Hybrid Tomato (Solanum lycopersicum) Under Flooding, Specialist, and Generalist Insect Herbivory, and their Stress Combination.Journal of chemical ecology · 2026Article
- Multi-Omics Reveals Domestication-Associated Shifts in Phosphorus Adaptation Strategies in Tomato.Plants (Basel, Switzerland) · 2026Article
- Genetic architecture of the tomato fruit lipidome.PNAS nexus · 2026Article
- A tomato MAGIC population reveals candidate genes for leaf dry matter and phenolics, two key traits for stress resilience and climate-smart breeding.Frontiers in plant science · 2026Article
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
- From greenhouse conditions to the field: stability of tolerance to water deficit in the tomato wild relatives Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium.BMC plant biology · 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
- What metabolomics has taught us about tomato fruit ripening and quality.Journal of experimental botany · 2025Review
- Allelic value in gene regulation-implications for gene editing.Annals of botany · 2025Article
- Distinct immune responses confer partial resistance to Fusarium wilt in tomato landraces.Planta · 2025Article
- Phylogenomic and super-pangenome analyses unveil the genetic landscape of tomato evolution and domestication.Plant biotechnology journal · 2025Article
- Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.Scientific reports · 2025Article
- New QTLs involved in the control of stigma position in tomato.BMC plant biology · 2025Article
- Molecular breeding of tomato: Advances and challenges.Journal of integrative plant biology · 2025Review
- Climate change-driven shifts in the global distribution of tomato and potato crops and their associated bacterial pathogens.Frontiers in microbiology · 2025Article
46 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDomestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection.
resultsOur results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and "cherry tomato" are not synonymous terms. The morphologically-based term "cherry tomato" included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups.
conclusionsThis study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement.
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