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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-835) contains supplementary material, which is available to authorized users.
Highlights
The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world
The cultivated tomato (Solanum lycopersicum L.) was probably domesticated in Mexico from wild species that originated in the Andean region, other hypotheses have been put forward [1]
Seventeen Single Nucleotide Polymorphism (SNP) were monomorphic among cultivated Solanum lycopersicum genotypes
Summary
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. The recent tomato genome sequencing indicated that several chromosomal segments within cultivated varieties are more closely related to S. pimpinellifolium than to Heinz 1706 The latter carries introgressions from S. pimpinellifolium, which has been used for the introduction of disease resistance traits, on several chromosomes (4, 9 11 and 12) [8]. Fruit size, colour and shape present a morphological variety absent in wild species [4], recent selection may have unintentionally diminished fruit quality in exchange for production traits [9]
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