ArticlePloS one2012
High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers, 1 of them a synthesis that pooled it.
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Who cites it
73 citing papers in PubMed, 1 synthesis or guideline pooled it, 167 citations in OpenAlex.
- Unraveling the genetic basis of quantitative resistance to diseases in tomato: a meta-QTL analysis and mining of transcript profiles.Plant cell reports · 2024Pooled it
- Detection and Utilisation of KASPar SNP Marker Assays for Early Blight Resistance in Tomato.Current microbiology · 2026Article
- An advanced 10K SNP panel for genotyping tomato (Frontiers in plant science · 2025Article
- Identification and Validation of Quantitative Trait Loci Associated with Fruit Puffiness in a Processing Tomato Population.Plants (Basel, Switzerland) · 2024Article
- Genetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers.PloS one · 2024Article
- Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family.Frontiers in plant science · 2024Review
- Molecular mapping of quantitative trait loci for resistance to early blight in tomatoes.Frontiers in plant science · 2023Article
- Diversity analyses in two ornamental and large-genomeFrontiers in plant science · 2023Article
- Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity Pool.International journal of molecular sciences · 2022Article
- European traditional tomatoes galore: a result of farmers' selection of a few diversity-rich loci.Journal of experimental botany · 2022Article
- Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red-fruited clade.The plant genome · 2022Article
- Evaluation of four methods to identify the homozygotic sex chromosome in small populations.BMC genomics · 2022Article
- Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato.Horticulture research · 2022Article
- An integrated genomic and biochemical approach to investigate the potentiality of heirloom tomatoes: Breeding resources for food quality and sustainable agriculture.Frontiers in plant science · 2022Article
- Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato.Computational and structural biotechnology journal · 2022Review
- Phenotypic and Genotypic Diversity of the Tomato Germplasm From the Lazio Region in Central Italy, With a Focus on Landrace Distinctiveness.Frontiers in plant science · 2022Article
- Genotyping Platforms for Genome-Wide Association Studies: Options and Practical Considerations.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Genome-wide association study identifies QTL for eight fruit traits in cultivated tomato (Solanum lycopersicum L.).Horticulture research · 2021Article
- Genetic diversity, population structure and validation of SSR markers linked toPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Cryptic introgressions contribute to transgressive segregation for early blight resistance in tomato.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 8 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA) and pairwise estimates of F(st) supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage), particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F(st) outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD) was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.