Show simple item record

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

hal.structure.identifierMeiji University
dc.contributor.authorKOBAYASHI, Masaaki
hal.structure.identifierNational Institute of Genetics [NIG]
dc.contributor.authorNAGASAKI, Hideki
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorGARCIA, Virginie
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorJUST, Daniel
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorBRES, Cécile
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorMAUXION, Jean-Philippe
hal.structure.identifierEtude du Polymorphisme des Génomes Végétaux [EPGV]
dc.contributor.authorLE PASLIER, Marie-Christine
hal.structure.identifierEtude du Polymorphisme des Génomes Végétaux [EPGV]
dc.contributor.authorBRUNEL, Dominique
hal.structure.identifierKazusa DNA Research Institute [KDRI]
dc.contributor.authorSUDA, Kunihiro
hal.structure.identifierNational Institute of Genetics [NIG]
dc.contributor.authorMINAKUCHI, Yohei
hal.structure.identifierNational Institute of Genetics [NIG]
dc.contributor.authorTOYODA, Atsushi
dc.contributor.authorFUJIYAMA, Asao
hal.structure.identifierMeiji University
dc.contributor.authorTOYOSHIMA, Hiromi
hal.structure.identifierMeiji University
dc.contributor.authorSUZUKI, Takayuki
hal.structure.identifierMeiji University
dc.contributor.authorIGARASHI, Kaori
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorROTHAN, Christophe
hal.structure.identifierNational Institute of Genetics [NIG]
dc.contributor.authorKAMINUMA, Eli
hal.structure.identifierNational Institute of Genetics [NIG]
dc.contributor.authorNAKAMURA, Yasukazu
hal.structure.identifierMeiji University
dc.contributor.authorYANO, Kentaro
hal.structure.identifierKazusa DNA Research Institute [KDRI]
dc.contributor.authorAOKI, Koh
dc.date.issued2014
dc.identifier.issn0032-0781
dc.description.abstractEnTomato (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 found in common between the two cultivars. The density of SNPs and indels was high in chromosomes 02, 05, and 11, but was low in chromosomes 06, 08 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.
dc.language.isoen
dc.publisherOxford University Press (OUP)
dc.subjectindels
dc.subject.enMicro-Tom
dc.subject.enSNPs
dc.subject.enSolanum lycopersicum
dc.subject.enTomato
dc.subject.engenome
dc.title.enGenome-wide analysis of intraspecific DNA polymorphism in 'Micro-Tom', a model cultivar of tomato (Solanum lycopersicum).
dc.typeArticle de revue
dc.identifier.doi10.1093/pcp/pct181
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
bordeaux.journalPlant and Cell Physiology
bordeaux.page445-454
bordeaux.volume55
bordeaux.issue2
bordeaux.peerReviewedoui
hal.identifierhal-02636501
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02636501v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Plant%20and%20Cell%20Physiology&rft.date=2014&rft.volume=55&rft.issue=2&rft.spage=445-454&rft.epage=445-454&rft.eissn=0032-0781&rft.issn=0032-0781&rft.au=KOBAYASHI,%20Masaaki&NAGASAKI,%20Hideki&GARCIA,%20Virginie&JUST,%20Daniel&BRES,%20C%C3%A9cile&rft.genre=article


Files in this item

FilesSizeFormatView

There are no files associated with this item.

This item appears in the following Collection(s)

Show simple item record