Genome-wide analysis of intraspecific DNA polymorphism in 'Micro-Tom', a model cultivar of tomato (Solanum lycopersicum)

Plant Cell Physiol. 2014 Feb;55(2):445-54. doi: 10.1093/pcp/pct181. Epub 2013 Dec 5.


Tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. The genome sequencing of the tomato cultivar 'Heinz 1706' was recently completed. To accelerate the progress of tomato genomics studies, systematic bioresources, such as mutagenized lines and full-length cDNA libraries, have been established for the cultivar 'Micro-Tom'. However, these resources cannot be utilized to their full potential without the completion of the genome sequencing of 'Micro-Tom'. We undertook the genome sequencing of 'Micro-Tom' and here report the identification of single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) between 'Micro-Tom' and 'Heinz 1706'. The analysis demonstrated the presence of 1.23 million SNPs and 0.19 million indels between the two cultivars. The density of SNPs and indels was high in chromosomes 2, 5 and 11, but was low in chromosomes 6, 8 and 10. Three known mutations of 'Micro-Tom' were localized on chromosomal regions where the density of SNPs and indels was low, which was consistent with the fact that these mutations were relatively new and introgressed into 'Micro-Tom' during the breeding of this cultivar. We also report SNP analysis for two 'Micro-Tom' varieties that have been maintained independently in Japan and France, both of which have served as standard lines for 'Micro-Tom' mutant collections. Approximately 28,000 SNPs were identified between these two 'Micro-Tom' lines. These results provide high-resolution DNA polymorphic information on 'Micro-Tom' and represent a valuable contribution to the 'Micro-Tom'-based genomics resources.

Keywords: Genome; Indels; Micro-Tom; SNPs; Solanum lycopersicum; Tomato.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breeding
  • Chromosome Mapping
  • DNA, Intergenic
  • DNA, Plant / chemistry
  • DNA, Plant / genetics
  • Gene Library
  • Genome, Plant / genetics*
  • Genomics
  • INDEL Mutation
  • Lycopersicon esculentum / genetics*
  • Molecular Sequence Annotation
  • Mutation
  • Phenotype
  • Polymorphism, Single Nucleotide*
  • Sequence Analysis, DNA
  • Species Specificity


  • DNA, Intergenic
  • DNA, Plant

Associated data

  • SRA/DRP000312.