ArticleBMC genomics2013
Tomato breeding in the genomics era: insights from a SNP array.
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 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 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
- Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding.Plants (Basel, Switzerland) · 2024Review
- Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives.Plants (Basel, Switzerland) · 2024Article
- Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family.Frontiers in plant science · 2024Review
- Improvement of crop production in controlled environment agriculture through breeding.Frontiers in plant science · 2024Review
- Diversity analyses in two ornamental and large-genomeFrontiers in plant science · 2023Article
- First genetic maps development and QTL mining inFrontiers in plant science · 2022Article
- The Genetic Basis of Tomato Aroma.Genes · 2021Review
- The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit.The Plant journal : for cell and molecular biology · 2020Article
- Identification of heat-tolerance QTLs and high-temperature stress-responsive genes through conventional QTL mapping, QTL-seq and RNA-seq in tomato.BMC plant biology · 2019Article
- Whole-Genome Resequencing of Seven Eggplant (Frontiers in plant science · 2019Article
- Breeding Has Increased the Diversity of Cultivated Tomato in The Netherlands.Frontiers in plant science · 2019Article
- Red Clover (Frontiers in plant science · 2018Article
- Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies.PloS one · 2017Article
- Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands.Frontiers in plant science · 2017Article
- Gene Classification and Mining of Molecular Markers Useful in Red Clover (Frontiers in plant science · 2017Article
- SNP-markers in Allium species to facilitate introgression breeding in onion.BMC plant biology · 2016Article
- Development and application of a novel genome-wide SNP array reveals domestication history in soybean.Scientific reports · 2016Article
- Identification of Loci Affecting Accumulation of Secondary Metabolites in Tomato Fruit of aFrontiers in plant science · 2016Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and high throughput genotyping. A set of 6000 SNPs was identified and 5528 of them were used to evaluate tomato germplasm at the level of species, varieties and segregating populations.
resultsFrom the 5528 SNPs, 1980 originated from 454-sequencing, 3495 from Illumina Solexa sequencing and 53 were additional known markers. Genotyping different tomato samples allowed the evaluation of the level of heterozygosity and introgressions among commercial varieties. Cherry tomatoes were especially different from round/beefs in chromosomes 4, 5 and 12. We were able to identify a set of 750 unique markers distinguishing S. lycopersicum 'Moneymaker' from all its distantly related wild relatives. Clustering and neighbour joining analysis among varieties and species showed expected grouping patterns, with S. pimpinellifolium as the most closely related to commercial tomatoes earlier results.
conclusionsOur results show that a SNP search in only a few breeding lines already provides generally applicable markers in tomato and its wild relatives. It also shows that the Illumina bead array generated data are highly reproducible. Our SNPs can roughly be divided in two categories: SNPs of which both forms are present in the wild relatives and in domesticated tomatoes (originating from common ancestors) and SNPs unique for the domesticated tomato (originating from after the domestication event). The SNPs can be used for genotyping, identification of varieties, comparison of genetic and physical linkage maps and to confirm (phylogenetic) relations. In the SNPs used for the array there is hardly any overlap with the SolCAP array and it is strongly recommended to combine both SNP sets and to select a core collection of robust SNPs completely covering the entire tomato genome.
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