ArticleG3 (Bethesda, Md.)2012
Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme.
Article in G3 (Bethesda, Md.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed.
- Haplotype-based genome-wide association study uncovers QTL for fruit-related traits in the 287 tomato accessions.BMC plant biology · 2026Article
- What metabolomics has taught us about tomato fruit ripening and quality.Journal of experimental botany · 2025Review
- New QTLs involved in the control of stigma position in tomato.BMC plant biology · 2025Article
- Genome-specific association study (GSAS) for exploration of variability in hemp (Cannabis sativa).Scientific reports · 2025Article
- Prediction accuracy of genomic estimated breeding values for fruit traits in cultivated tomato (Solanum lycopersicum L.).BMC plant biology · 2024Article
- Mechanisms of salinity tolerance and their possible application in the breeding of vegetables.BMC plant biology · 2023Review
- Review
- Genome wide association mapping for agronomic, fruit quality, and root architectural traits in tomato under organic farming conditions.BMC plant biology · 2021Article
- Genome-wide association study identifies QTL for eight fruit traits in cultivated tomato (Solanum lycopersicum L.).Horticulture research · 2021Article
- Genomic and Phenotypic Diversity of Cultivated and Wild Tomatoes with Varying Levels of Heat Tolerance.Genes · 2021Article
- Cultivated Tomato (Plants (Basel, Switzerland) · 2020Article
- Review
- Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal phenotypic evolvability despite pervasive epistasis.PLoS computational biology · 2020Article
- Advances and Challenges in Bacterial Spot Resistance Breeding in Tomato (International journal of molecular sciences · 2020Review
- Assessment of Genetic Differentiation and Linkage Disequilibrium inG3 (Bethesda, Md.) · 2019Article
- Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Frontiers in plant science · 2018Article
- Quantitative trait loci from identification to exploitation for crop improvement.Plant cell reports · 2017Review
- Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial FTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- 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
- Article
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10 authors.
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Abstract
Genome-wide association mapping is an efficient way to identify quantitative trait loci controlling the variation of phenotypes, but the approach suffers severe limitations when one is studying inbred crops like cultivated tomato (Solanum lycopersicum). Such crops exhibit low rates of molecular polymorphism and high linkage disequilibrium, which reduces mapping resolution. The cherry type tomato (S. lycopersicum var. cerasiforme) genome has been described as an admixture between the cultivated tomato and its wild ancestor, S. pimpinellifolium. We have thus taken advantage of the properties of this admixture to improve the resolution of association mapping in tomato. As a proof of concept, we sequenced 81 DNA fragments distributed on chromosome 2 at different distances in a core collection of 90 tomato accessions, including mostly cherry type tomato accessions. The 81 Sequence Tag Sites revealed 352 SNPs and indels. Molecular diversity was greatest for S. pimpinellifolium accessions, intermediate for S. l. cerasiforme accessions, and lowest for the cultivated group. We assessed the structure of molecular polymorphism and the extent of linkage disequilibrium over genetic and physical distances. Linkage disequilibrium decreased under r(2) = 0.3 within 1 cM, and minimal estimated value (r(2) = 0.13) was reached within 20 kb over the physical regions studied. Associations between polymorphisms and fruit weight, locule number, and soluble solid content were detected. Several candidate genes and quantitative trait loci previously identified were validated and new associations detected. This study shows the advantages of using a collection of S. l. cerasiforme accessions to overcome the low resolution of association mapping in tomato.
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