title: A whole-genome analysis of a transgenic rice seed-based edible vaccine against cedar pollen allergy.
abstract: Genetic modification (GM) by Agrobacterium-mediated transformation is a robust and widely employed method to confer new traits to crops. In this process, a transfer DNA is delivered into the host genome, but it is still unclear how the host genome is altered by this event at single-base resolution. To decipher genomic discrepancy between GM crops and their host, we conducted whole-genome sequencing of a transgenic rice line OSCR11. This rice line expresses a seed-based edible vaccine containing two major pollen allergens, Cry j 1 and Cry j 2, against Japanese cedar pollinosis. We revealed that genetic differences between OSCR11 and its host a123 were significantly less than those between a123 and its precedent cultivar Koshihikari. The pattern of nucleotide base substitution in OSCR11, relative to a123, was consistent with somaclonal variation. Mutations in OSCR11 probably occurred during the cell culture steps. In addition, strand-specific mRNA-Seq revealed similar transcriptomes of a123 and OSCR11, supporting genomic integrity between them.
authors: 1Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kan-nondai, Tsukuba, Ibaraki 305-8602, Japan.
authors: Taiji
authors: T
authors: Kawakatsu
authors: Yoshihiro
authors: Y
authors: Kawahara
authors: Takeshi
authors: T
authors: Itoh
authors: Fumio
authors: F
authors: Takaiwa
mesh_terms: D060054:Agrobacterium / Q000235:genetics; D052179:Antigens, Plant / Q000235:genetics; D028203:Cedrus / Q000276:immunology*; D018745:Genome, Plant; D059645:Mutation Rate; D012275:Oryza / Q000235:genetics / Q000276:immunology*; D010940:Plant Proteins / Q000235:genetics; D030821:Plants, Genetically Modified / Q000235:genetics / Q000276:immunology; D011110:Polymorphism, Genetic; D006255:Rhinitis, Allergic, Seasonal / Q000276:immunology / Q000517:prevention & control*; D012639:Seeds / Q000235:genetics / Q000276:immunology*; D017422:Sequence Analysis, DNA; D059467:Transcriptome; D022462:Vaccines, Edible / Q000235:genetics* / Q000276:immunology
chemical_list: D052179:Antigens, Plant; C065290:Cry j I protein, Cryptomeria japonica; C065291:Cry j II protein, Cryptomeria japonica; D010940:Plant Proteins; D022462:Vaccines, Edible
keywords: GM crop; cedar pollen allergy; transcriptome; transgenic rice; whole-genome sequence
references: Plant Cell Physiol. 2012 Apr;53(4):755-61
references: 22327484
references: Plant Biotechnol J. 2013 Jan;11(1):66-76
references: 23066780
references: Plant J. 2011 Apr;66(2):241-6
references: 21219509
references: Plant Biotechnol J. 2003 Nov;1(6):411-22
references: 17134400
references: Genes Genet Syst. 2009 Oct;84(5):361-70
references: 20154423
references: Science. 2001 Dec 14;294(5550):2317-23
references: 11743193
references: Plant Biotechnol J. 2010 Aug;8(6):691-718
references: 20331531
references: Plant J. 2012 Mar;69(6):946-56
references: 22050533
references: Plant Cell Physiol. 2013 Feb;54(2):e6
references: 23299411
references: Science. 2010 Jan 1;327(5961):92-4
references: 20044577
references: Nat Biotechnol. 2002 Oct;20(10):1030-4
references: 12219079
references: Nat Biotechnol. 2011 Jan;29(1):24-6
references: 21221095
references: Nat Biotechnol. 2008 Sep;26(9):1015-7
references: 18758448
references: Annu Rev Phytopathol. 2010;48:45-68
references: 20337518
references: Mol Cells. 2012 Jun;33(6):583-9
references: 22570148
references: Bioinformatics. 2009 Jul 15;25(14):1754-60
references: 19451168
references: Nat Biotechnol. 2012 May 07;30(5):390-2
references: 22565958
references: Plant Cell Physiol. 2011 Feb;52(2):274-82
references: 21258067
references: Genetics. 2003 Jun;164(2):731-40
references: 12807792
references: Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3640-5
references: 18303117
references: Nature. 2008 Apr 24;452(7190):991-6
references: 18432245
references: Annu Rev Plant Biol. 2011;62:1-23
references: 21314429
references: Curr Biol. 2011 Aug 23;21(16):1385-90
references: 21802297
references: Plant Cell Physiol. 2012 Jan;53(1):256-64
references: 22156226
references: Theor Appl Genet. 2004 Nov;109(7):1512-8
references: 15300384
references: Genome Biol. 2010;11(10):R106
references: 20979621
references: Plant J. 2010 Sep;63(6):990-1003
references: 20626650
references: BMC Genomics. 2010 Apr 27;11:267
references: 20423466