ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2014
In silico identification and experimental validation of insertion-deletion polymorphisms in tomato genome.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- A single nucleotide substitution in the SlMCT gene contributes to great morphological alternations in tomato.Molecular horticulture · 2025Article
- Development of novel InDel markers by whole-genome sequence comparison and genetic diversity assessment of Thailand rice blast fungus populations.Stress biology · 2025Article
- Identification of Insertion and Deletion (InDel) Markers for Chickpea (Plants (Basel, Switzerland) · 2024Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Molecular Characterization and Genetic Diversity of Ginkgo (Plants (Basel, Switzerland) · 2023Article
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- Plasticity of maternal environment-dependent expression-QTLs of tomato seeds.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Vegetable biology and breeding in the genomics era.Science China. Life sciences · 2023Review
- Development of Omni InDel and supporting database for maize.Frontiers in plant science · 2023Article
- Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars.Plant cell reports · 2022Article
- Mapping and characterization of the Rx3 gene for resistance to Xanthomonas euvesicatoria pv. euvesicatoria race T1 in tomato.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Genome-Wide Discovery of InDel Markers in Sesame (Plants (Basel, Switzerland) · 2020Article
- Transcription of lncRNARNA biology · 2020Article
- IDSSR: An Efficient Pipeline for Identifying Polymorphic Microsatellites from a Single Genome Sequence.International journal of molecular sciences · 2019Article
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- Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits.BMC plant biology · 2018Article
- Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.).BMC genomics · 2017Article
- Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the GenusFrontiers in plant science · 2017Article
- Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers.Frontiers in plant science · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparative analysis of the genome sequences of Solanum lycopersicum variety Heinz 1706 and S. pimpinellifolium accession LA 1589 using MUGSY software identified 145 695 insertion-deletion (InDel) polymorphisms. A selected set of 3029 candidate InDels (≥2 bp) across the entire tomato genome were subjected to PCR validation, and 82.4% could be verified. Of 2272 polymorphic InDels between LA 1589 and Heinz 1706, 61.6, 45.2, and 31.6% were polymorphic in 8 accessions of S. pimpinellifolium, 4 accessions of S. lycopersicum var. cerasiforme, and 10 varieties of S. lycopersicum, respectively. Genetic distance was 0.216 in S. pimpinellifolium, 0.202 in S. lycopersicum var. cerasiforme, and 0.108 in S. lycopersicum. The data suggested a reduction of genetic variation from S. pimpinellifolium to S. lycopersicum var. cerasiforme and S. lycopersicum. Cluster analysis showed that the 8 accessions of S. pimpinellifolium were in one group, whereas 4 accessions of S. lycopersicum var. cerasiforme and 10 varieties of S. lycopersicum were in the same group.
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