Whole genome resequencing in tomato reveals variation associated with introgression and breeding events
Abstract
BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.
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BibTeX
@article{causse2026whole,
title = {{Whole genome resequencing in tomato reveals variation associated with introgression and breeding events}},
author = {Mathilde Causse and Nelly Desplat and Laura Pascual and Marie-Christine Le Paslier and Christopher Sauvage and Guillaume Bauchet and Aurélie Bérard and Rémi Bounon and Maria Tchoumakov and Dominique Brunel and Jean-Paul Bouchet},
journal = {BMC Genomics},
year = {2026},
month = sep,
doi = {10.1186/1471-2164-14-791},
url = {https://hal.science/hal-05772128v1},
note = {CC BY},
}
RIS
TY - JOUR
TI - Whole genome resequencing in tomato reveals variation associated with introgression and breeding events
AU - Mathilde Causse
AU - Nelly Desplat
AU - Laura Pascual
AU - Marie-Christine Le Paslier
AU - Christopher Sauvage
AU - Guillaume Bauchet
AU - Aurélie Bérard
AU - Rémi Bounon
AU - Maria Tchoumakov
AU - Dominique Brunel
AU - Jean-Paul Bouchet
PY - 2026
DA - 2026/09/30
JO - BMC Genomics
DO - 10.1186/1471-2164-14-791
UR - https://hal.science/hal-05772128v1
AB - BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.
SN - 1471-2164
ER -