ArticleBMC genomics2013
SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato.
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 21 papers.
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Who cites it
21 citing papers in PubMed.
- Genetic diversity and population structure analysis in Asparagus officinalis.Journal, genetic engineering & biotechnology · 2025Article
- Characterization of Indian waxy and non-waxy maize germplasm for genetic differentiation through SNP genotyping.Molecular genetics and genomics : MGG · 2025Article
- Rhizosphere Microbiome Co-Occurrence Network Analysis across a Tomato Domestication Gradient.Microorganisms · 2024Article
- Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding.Plants (Basel, Switzerland) · 2024Review
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- Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato.Computational and structural biotechnology journal · 2022Review
- Cultivated Tomato (Plants (Basel, Switzerland) · 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
- Morphological and genetic differences between Coptis japonica var. anemonifolia H. Ohba and Coptis japonica var. major Satake in Hokuriku area.Journal of natural medicines · 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
- Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape.Frontiers in plant science · 2017Review
- In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits.PloS one · 2017Article
- Comparison of Genetic Diversity between Chinese and American Soybean (Frontiers in plant science · 2017Article
- In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations.Scientific reports · 2016Article
- Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing.BMC genomics · 2016Article
- Identification of Genetic Differentiation between Waxy and Common Maize by SNP Genotyping.PloS one · 2015Article
- Exploring a Tomato Landraces Collection for Fruit-Related Traits by the Aid of a High-Throughput Genomic Platform.PloS one · 2015Article
- Article
- Genome-wide characterization of genetic diversity and population structure in Secale.BMC plant biology · 2014Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes.
resultsWith the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties.
conclusionsOur work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs.
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