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SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato
BACKGROUND: The 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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046682/ https://www.ncbi.nlm.nih.gov/pubmed/24279304 http://dx.doi.org/10.1186/1471-2164-14-835 |
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author | Corrado, Giandomenico Piffanelli, Pietro Caramante, Martina Coppola, Mariangela Rao, Rosa |
author_facet | Corrado, Giandomenico Piffanelli, Pietro Caramante, Martina Coppola, Mariangela Rao, Rosa |
author_sort | Corrado, Giandomenico |
collection | PubMed |
description | BACKGROUND: The 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. RESULTS: With 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. CONCLUSIONS: Our 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-14-835) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4046682 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40466822014-06-06 SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato Corrado, Giandomenico Piffanelli, Pietro Caramante, Martina Coppola, Mariangela Rao, Rosa BMC Genomics Research Article BACKGROUND: The 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. RESULTS: With 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. CONCLUSIONS: Our 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-14-835) contains supplementary material, which is available to authorized users. BioMed Central 2013-11-27 /pmc/articles/PMC4046682/ /pubmed/24279304 http://dx.doi.org/10.1186/1471-2164-14-835 Text en © Corrado et al.; licensee BioMed Central Ltd. 2013 This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Corrado, Giandomenico Piffanelli, Pietro Caramante, Martina Coppola, Mariangela Rao, Rosa SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato |
title | SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato |
title_full | SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato |
title_fullStr | SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato |
title_full_unstemmed | SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato |
title_short | SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato |
title_sort | snp genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046682/ https://www.ncbi.nlm.nih.gov/pubmed/24279304 http://dx.doi.org/10.1186/1471-2164-14-835 |
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