ArticlePloS one2012
Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.
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 155 papers, 2 of them syntheses that pooled it.
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Who cites it
155 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- 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
- Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor.Nature communications · 2019Pooled it
- Polymorphism can extensively reshape the genome-wide crossover landscape in Arabidopsis thaliana.Nature communications · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- Detection and Utilisation of KASPar SNP Marker Assays for Early Blight Resistance in Tomato.Current microbiology · 2026Article
- Fine-mapping and candidate gene analysis of qFF3.1 conferring fruit firmness in a modern tomato variety.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- ExploringTy resistance genes and genetic diversity in improved tomato lines selected from commercial hybrids.BMC plant biology · 2025Article
- Identification of late blight resistance QTLsMolecular breeding : new strategies in plant improvement · 2025Article
- An advanced 10K SNP panel for genotyping tomato (Frontiers in plant science · 2025Article
- Advances in genomic tools for plant breeding: harnessing DNA molecular markers, genomic selection, and genome editing.Biological research · 2024Review
- Identification and mapping of late blight resistance QTLs in the wild tomato accession PI 224710 (Molecular breeding : new strategies in plant improvement · 2024Article
- Whole genome sequence data of 516 FData in brief · 2024Article
- A catalogue of recombination coldspots in interspecific tomato hybrids.PLoS genetics · 2024Article
- Identification and Validation of Quantitative Trait Loci Associated with Fruit Puffiness in a Processing Tomato Population.Plants (Basel, Switzerland) · 2024Article
- Genetic tapestry of Capsicum fruit colors: a comparative analysis of four cultivated species.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Genome-wide variants and optimal allelic combinations for citric acid in tomato.Horticulture research · 2024Article
- Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives.Plants (Basel, Switzerland) · 2024Article
- Genomic Analysis of Romanian Lycium Genotypes: ExploringInternational journal of molecular sciences · 2024Article
- Wheat Water-Soluble Carbohydrate Remobilisation under Water Deficit byCurrent issues in molecular biology · 2023Article
- The regulation of meiotic crossover distribution: a coarse solution to a century-old mystery?Biochemical Society transactions · 2023Review
95 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F(2) populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.
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