ArticleBMC genomics2013
Whole genome resequencing in tomato reveals variation associated with introgression and breeding events.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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63 citing papers in PubMed.
- Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes.bioRxiv : the preprint server for biology · 2025Article
- New QTLs involved in the control of stigma position in tomato.BMC plant biology · 2025Article
- Combining Transcriptome and Whole Genome Re-Sequencing to Screen Disease Resistance Genes for Wheat Dwarf Bunt.International journal of molecular sciences · 2023Article
- Diversity and genetic architecture of agro-morphological traits in a core collection of European traditional tomato.Journal of experimental botany · 2023Article
- Article
- Next-Generation Sequencing of Local Romanian Tomato Varieties and Bioinformatics Analysis of theInternational journal of molecular sciences · 2022Article
- Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea chilensis) Using GBS Tools.Plants (Basel, Switzerland) · 2022Article
- Sorghum Association Panel whole-genome sequencing establishes cornerstone resource for dissecting genomic diversity.The Plant journal : for cell and molecular biology · 2022Article
- European traditional tomatoes galore: a result of farmers' selection of a few diversity-rich loci.Journal of experimental botany · 2022Article
- Whole-genome resequencing of Sorghum bicolor and S. bicolor × S. halepense lines provides new insights for improving plant agroecological characteristics.Scientific reports · 2022Article
- Genome-wide exploration of oil biosynthesis genes in cultivated olive tree varieties (Olea europaea): insights into regulation of oil biosynthesis.Functional & integrative genomics · 2022Article
- Whole-genome resequencing reveals genomic footprints of Italian sweet and hot pepper heirlooms giving insight into genes underlying key agronomic and qualitative traits.BMC genomic data · 2022Article
- Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato.Horticulture research · 2022Article
- Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato.Computational and structural biotechnology journal · 2022Review
- Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions.Quantitative plant biology · 2022Review
- Exploring the diversity of promoter and 5'UTR sequences in ancestral, historic and modern wheat.Plant biotechnology journal · 2021Article
- A systems genetics approach to deciphering the effect of dosage variation on leaf morphology in Populus.The Plant cell · 2021Article
- Effects of water deficit on leaves and fruit quality during the development period in tomato plant.Food science & nutrition · 2021Article
- Editorial: Introgression Breeding in Cultivated Plants.Frontiers in plant science · 2021Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
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Abstract
backgroundOne of the goals of genomics is to identify the genetic loci responsible for variation in phenotypic traits. The completion of the tomato genome sequence and recent advances in DNA sequencing technology allow for in-depth characterization of genetic variation present in the tomato genome. Like many self-pollinated crops, cultivated tomato accessions show a low molecular but high phenotypic diversity. Here we describe the whole-genome resequencing of eight accessions (four cherry-type and four large fruited lines) chosen to represent a large range of intra-specific variability and the identification and annotation of novel polymorphisms.
resultsThe eight genomes were sequenced using the GAII Illumina platform. Comparison of the sequences with the reference genome yielded more than 4 million single nucleotide polymorphisms (SNPs). This number varied from 80,000 to 1.5 million according to the accessions. Almost 128,000 InDels were detected. The distribution of SNPs and InDels across and within chromosomes was highly heterogeneous revealing introgressions from wild species and the mosaic structure of the genomes of the cherry tomato accessions. In-depth annotation of the polymorphisms identified more than 16,000 unique non-synonymous SNPs. In addition 1,686 putative copy-number variations (CNVs) were identified.
conclusionsThis study represents the first whole genome resequencing experiment in cultivated tomato. Substantial genetic differences exist between the sequenced tomato accessions and the reference sequence. The heterogeneous distribution of the polymorphisms may be related to introgressions that occurred during domestication or breeding. The annotated SNPs, InDels and CNVs identified in this resequencing study will serve as useful genetic tools, and as candidate polymorphisms in the search for phenotype-altering DNA variations.
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