ArticleJournal of experimental botany2011
Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato.
Article in Journal of experimental botany, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it, 88 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
- Multi-locus genome-wide association studies for root system architectural traits in Ethiopian sorghum (Sorghum bicolor L.) landraces.BMC plant biology · 2025Article
- Effect of Postharvest Storage Temperature and Duration on Tomato Fruit Quality.Foods (Basel, Switzerland) · 2025Article
- RiceSNP-ABST: a deep learning approach to identify abiotic stress-associated single nucleotide polymorphisms in rice.Briefings in bioinformatics · 2024Article
- Auxin-driven ecophysiological diversification of leaves in domesticated tomato.Plant physiology · 2022Article
- Article
- 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
- Increased branching independent of strigolactone in cytokinin oxidase 2-overexpressing tomato is mediated by reduced auxin transport.Molecular horticulture · 2022Article
- Modeling allelic diversity of multiparent mapping populations affects detection of quantitative trait loci.G3 (Bethesda, Md.) · 2022Article
- Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato.Horticulture research · 2022Article
- Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (International journal of molecular sciences · 2021Article
- How the pan-genome is changing crop genomics and improvement.Genome biology · 2021Review
- ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean 'da serbo' type long shelf-life germplasm.Horticulture research · 2020Article
- Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers.Frontiers in plant science · 2017Article
- Article
- Exploring a Tomato Landraces Collection for Fruit-Related Traits by the Aid of a High-Throughput Genomic Platform.PloS one · 2015Article
- An association mapping approach to identify favourable alleles for tomato fruit quality breeding.BMC plant biology · 2014Article
- Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins.BMC plant biology · 2014Article
- Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant.BMC genomics · 2014Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The history of tomato (Solanum lycopersicum L.) improvement includes genetic bottlenecks, wild species introgressions, and divergence into distinct market classes. This history makes tomato an excellent model to investigate the effects of selection on genome variation. A combination of linkage mapping in two F(2) populations and physical mapping with emerging genome sequence data was used to position 434 PCR-based markers including SNPs. Three-hundred-and-forty markers were used to genotype 102 tomato lines representing wild species, landraces, vintage cultivars, and contemporary (fresh market and processing) varieties. Principal component analysis confirmed genetic divergence between market classes of cultivated tomato (P <0.0001). A genome-wide survey indicated that linkage disequilibrium (LD) decays over 6-8 cM when all cultivated tomatoes, including vintage and contemporary, were considered together. Within contemporary processing varieties, LD decayed over 6-14 cM, and decay was over 3-16 cM within fresh market varieties. Significant inter-chromosomal (gametic phase) LD was detected in both fresh market and processing varieties between chromosomes 2 and 3, and 2 and 4, but in distinct chromosomal locations for each market class. Additional LD was detected between chromosomes 3 and 4, 3 and 11, and 4 and 6 in fresh market varieties and chromosomes 3 and 12 in processing varieties. These results suggest that breeding practices for market specialization in tomato have led to a genetic divergence between fresh market and processing types.
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