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

作者：Mathilde Causse, Nelly Desplat, Laura Pascual, Marie‐Christine Le Paslier, Christopher Sauvage, Guillaume Bauchet, Aurélie Berard, Rémi Bounon, Maria Tchoumakov, Dominique Brunel, Jean‐Paul Bouchet · 发表于：BMC Genomics · 年份：2013 · DOI：10.1186/1471-2164-14-791 · 被引用次数：146 · 研究领域：Chromosomal and Genetic Variations、Genetic Mapping and Diversity in Plants and Animals、Advances in Cucurbitaceae Research

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 s...