ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2017
Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 58 citations in OpenAlex.
- Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor.Nature communications · 2019Pooled it
- Genome Wide Association Study Reveals Novel Loci Controlling Agronomic Traits in Tomato (Solanum lycopersicum L.).Biochemical genetics · 2026Article
- From data to decisions: a paradigm shift in fruit agriculture through the integration of multi-omics, modern phenotyping, and cutting-edge bioinformatic tools.Frontiers in plant science · 2025Review
- Genome-Wide Association Study (GWAS) for Identifying SNPs and Genes Related to Phosphate-Induced Phenotypic Traits in Tomato (Plants (Basel, Switzerland) · 2024Article
- Mapping phenotypic performance and novel SNPs for cold tolerance in tomato (Solanum lycopersicum) genotypes through GWAS and population genetics.BMC genomic data · 2024Article
- Understanding tobamovirus-plant interactions: implications for breeding resistance to tomato brown rugose fruit virus.Journal of plant pathology : an international journal of the Italian Phytopathological Society · 2023Review
- Mitochondrial genomes do not appear to regulate flowering pattern/reproductive strategy inAoB PLANTS · 2022Article
- De novo SNP calling reveals the genetic differentiation and morphological divergence in genus Amaranthus.The plant genome · 2022Article
- The INRAE Centre for Vegetable Germplasm: Geographically and Phenotypically Diverse Collections and Their Use in Genetics and Plant Breeding.Plants (Basel, Switzerland) · 2022Article
- Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato.Computational and structural biotechnology journal · 2022Review
- Genome wide association mapping for agronomic, fruit quality, and root architectural traits in tomato under organic farming conditions.BMC plant biology · 2021Article
- Morphological Diversity, Genetic Characterization, and Phytochemical Assessment of the Cypriot Tomato Germplasm.Plants (Basel, Switzerland) · 2021Article
- Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- The Genetic Basis of Tomato Aroma.Genes · 2021Review
- Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects.International journal of molecular sciences · 2021Review
- Dissection of complex traits of tomato in the post-genome era.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Advances and Challenges in Bacterial Spot Resistance Breeding in Tomato (International journal of molecular sciences · 2020Review
- Exploiting the diversity of tomato: the development of a phenotypically and genetically detailed germplasm collection.Horticulture research · 2020Article
- 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
- Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis.BMC genomics · 2019Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageA panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato. Until now GWAS in tomato has been performed on panels of heirloom and wild accessions. Using modern breeding materials would be of direct interest for breeding purpose. To implement GWAS on a large panel of 300 tomato accessions including 168 breeding lines, this study assessed the genetic diversity and linkage disequilibrium decay and revealed the population structure and performed GWA experiment. Genetic diversity and population structure analyses were based on molecular markers (>11,000 SNP) covering the whole genome. Six genetic subgroups were revealed and associated to traits of agronomical interest, such as fruit weight and disease resistance. Estimates of linkage disequilibrium highlighted the heterogeneity of its decay among genetic subgroups. Haplotype definition allowed a fine characterization of the groups and their recombination landscape revealing the patterns of admixture along the genome. Selection footprints showed results in congruence with introgressions. Taken together, all these elements refined our knowledge of the genetic material included in this panel and allowed the identification of several associations for fruit weight, plant growth and earliness, deciphering the genetic architecture of these complex traits and identifying several new loci useful for tomato breeding.
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