title: Genome-wide analysis of intraspecific DNA polymorphism in 'Micro-Tom', a model cultivar of tomato (Solanum lycopersicum).
abstract: 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.
authors: Faculty of Agriculture, Meiji University, 1-1-1 Higashi Mita, Tama-ku, Kawasaki, 214-8571 Japan.
authors: Masaaki
authors: M
authors: Kobayashi
authors: Hideki
authors: H
authors: Nagasaki
authors: Virginie
authors: V
authors: Garcia
authors: Daniel
authors: D
authors: Just
authors: Cécile
authors: C
authors: Bres
authors: Jean-Philippe
authors: JP
authors: Mauxion
authors: Marie-Christine
authors: MC
authors: Le Paslier
authors: Dominique
authors: D
authors: Brunel
authors: Kunihiro
authors: K
authors: Suda
authors: Yohei
authors: Y
authors: Minakuchi
authors: Atsushi
authors: A
authors: Toyoda
authors: Asao
authors: A
authors: Fujiyama
authors: Hiromi
authors: H
authors: Toyoshima
authors: Takayuki
authors: T
authors: Suzuki
authors: Kaori
authors: K
authors: Igarashi
authors: Christophe
authors: C
authors: Rothan
authors: Eli
authors: E
authors: Kaminuma
authors: Yasukazu
authors: Y
authors: Nakamura
authors: Kentaro
authors: K
authors: Yano
authors: Koh
authors: K
authors: Aoki
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D021901:DNA, Intergenic; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D054643:INDEL Mutation; D018551:Solanum lycopersicum / Q000235:genetics*; D058977:Molecular Sequence Annotation; D009154:Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D021901:DNA, Intergenic; D018744:DNA, Plant
keywords: Genome; Indels; Micro-Tom; SNPs; Solanum lycopersicum; Tomato