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Genome-wide SNP genotyping to infer the effects on gene functions in tomato.

hal.structure.identifierKazusa DNA Research Institute [KDRI]
dc.contributor.authorHIRAKAWA, Hideki
hal.structure.identifierKazusa DNA Research Institute [KDRI]
dc.contributor.authorSHIRASAWA, Kenta
hal.structure.identifierNARO Institute of Vegetable and Tea Science
dc.contributor.authorOHYAMA, Akio
hal.structure.identifierNARO Institute of Vegetable and Tea Science
dc.contributor.authorFUKUOKA, Hiroyuki
hal.structure.identifierOsaka University
dc.contributor.authorAOKI, Koh
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorROTHAN, Christophe
hal.structure.identifierKazusa DNA Research Institute [KDRI]
dc.contributor.authorSATO, Shusei
hal.structure.identifierKazusa DNA Research Institute [KDRI]
dc.contributor.authorISOBE, Sachiko
hal.structure.identifierKazusa DNA Research Institute [KDRI]
dc.contributor.authorTABATA, Satoshi
dc.date.issued2013
dc.identifier.issn1340-2838
dc.description.abstractEnThe genotype data of 7054 single nucleotide polymorphism (SNP) loci in 40 tomato lines, including inbred lines, F1 hybrids, and wild relatives, were collected using Illumina's Infinium and GoldenGate assay platforms, the latter of which was utilized in our previous study. The dendrogram based on the genotype data corresponded well to the breeding types of tomato and wild relatives. The SNPs were classified into six categories according to their positions in the genes predicted on the tomato genome sequence. The genes with SNPs were annotated by homology searches against the nucleotide and protein databases, as well as by domain searches, and they were classified into the functional categories defined by the NCBI's eukaryotic orthologous groups (KOG). To infer the SNPs' effects on the gene functions, the three-dimensional structures of the 843 proteins that were encoded by the genes with SNPs causing missense mutations were constructed by homology modelling, and 200 of these proteins were considered to carry non-synonymous amino acid substitutions in the predicted functional sites. The SNP information obtained in this study is available at the Kazusa Tomato Genomics Database (http://plant1.kazusa.or.jp/tomato/).
dc.language.isoen
dc.publisherOxford University Press (OUP)
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enSolanum lycopersicum
dc.subject.engoldengate assay
dc.subject.enhomology modelling
dc.subject.eninfinium assay
dc.subject.ensingle nucleotide polymorphism (SNP)
dc.title.enGenome-wide SNP genotyping to infer the effects on gene functions in tomato.
dc.typeArticle de revue
dc.identifier.doi10.1093/dnares/dst005
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
bordeaux.journalDNA Research
bordeaux.page221-33
bordeaux.volume20
bordeaux.issue3
bordeaux.peerReviewedoui
hal.identifierhal-02647017
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02647017v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=DNA%20Research&rft.date=2013&rft.volume=20&rft.issue=3&rft.spage=221-33&rft.epage=221-33&rft.eissn=1340-2838&rft.issn=1340-2838&rft.au=HIRAKAWA,%20Hideki&SHIRASAWA,%20Kenta&OHYAMA,%20Akio&FUKUOKA,%20Hiroyuki&AOKI,%20Koh&rft.genre=article


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