Open Access Highly Accessed Research article

Whole genome resequencing in tomato reveals variation associated with introgression and breeding events

Mathilde Causse1*, Nelly Desplat14, Laura Pascual1, Marie-Christine Le Paslier2, Christopher Sauvage1, Guillaume Bauchet13, Aurélie Bérard2, Rémi Bounon2, Maria Tchoumakov2, Dominique Brunel2 and Jean-Paul Bouchet1

Author Affiliations

1 INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, BP94, Montfavet F-84143, France

2 US1279 INRA, Etude du Polymorphisme des Génomes Végétaux, CEA-Institut de Génomique-Centre National de Génotypage, Evry 91057, France

3 Syngenta Seeds 12, chemin de l’Hobit, Saint-Sauveur 31790, France

4 ND present address: BIOGEMMA, Centre de Recherche de Chappes, CS 90126, Chappes 63720, France

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BMC Genomics 2013, 14:791  doi:10.1186/1471-2164-14-791

Published: 14 November 2013



One of the goals of genomics is to identify the genetic loci responsible for variation in phenotypic traits. The completion of the tomato genome sequence and recent advances in DNA sequencing technology allow for in-depth characterization of genetic variation present in the tomato genome. Like many self-pollinated crops, cultivated tomato accessions show a low molecular but high phenotypic diversity. Here we describe the whole-genome resequencing of eight accessions (four cherry-type and four large fruited lines) chosen to represent a large range of intra-specific variability and the identification and annotation of novel polymorphisms.


The eight genomes were sequenced using the GAII Illumina platform. Comparison of the sequences with the reference genome yielded more than 4 million single nucleotide polymorphisms (SNPs). This number varied from 80,000 to 1.5 million according to the accessions. Almost 128,000 InDels were detected. The distribution of SNPs and InDels across and within chromosomes was highly heterogeneous revealing introgressions from wild species and the mosaic structure of the genomes of the cherry tomato accessions. In-depth annotation of the polymorphisms identified more than 16,000 unique non-synonymous SNPs. In addition 1,686 putative copy-number variations (CNVs) were identified.


This study represents the first whole genome resequencing experiment in cultivated tomato. Substantial genetic differences exist between the sequenced tomato accessions and the reference sequence. The heterogeneous distribution of the polymorphisms may be related to introgressions that occurred during domestication or breeding. The annotated SNPs, InDels and CNVs identified in this resequencing study will serve as useful genetic tools, and as candidate polymorphisms in the search for phenotype-altering DNA variations.

Tomato; Genome; Sequence; Single nucleotide polymorphism; Introgression