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PMID: 14630961 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Generation and analysis of end sequence database for T-DNA tagging lines in rice.

Plant physiology ·Vol. 133 ·No. 4 ·2003-12-00 ·Pages 2040-7

An S, Park S, Jeong DH, Lee DY, Kang HG, Yu JH, Hur J, Kim SR, Kim YH, Lee M, Han S, Kim SJ, Yang J, Kim E, Wi SJ, Chung HS, Hong JP, Choe V, Lee HK, Choi JH, Nam J, Kim SR, Park PB, Park KY, Kim WT, Choe S, Lee CB, An G

Abstract

We analyzed 6749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3793 genomic sequences flanking the T-DNA. Among the insertions, 1846 T-DNAs were integrated into genic regions, and 1864 were located in intergenic regions. Frequencies were also higher at the beginning and end of the coding regions and upstream near the ATG start codon. The overall GC content at the insertion sites was close to that measured from the entire rice (Oryza sativa) genome. Functional classification of these 1846 tagged genes showed a distribution similar to that observed for all the genes in the rice chromosomes. This indicates that T-DNA insertion is not biased toward a particular class of genes. There were 764, 327, and 346 T-DNA insertions in chromosomes 1, 4 and 10, respectively. Insertions were not evenly distributed; frequencies were higher at the ends of the chromosomes and lower near the centromere. At certain sites, the frequency was higher than in the surrounding regions. This sequence database will be valuable in identifying knockout mutants for elucidating gene function in rice. This resource is available to the scientific community at http://www.postech.ac.kr/life/pfg/risd.

MeSH Terms
Base Sequence DNA Primers DNA, Bacterial/chemistry,genetics DNA, Single-Stranded/genetics Exons Genetic Vectors Introns Mutagenesis, Insertional Oryza/genetics Plants, Genetically Modified/genetics Polymerase Chain Reaction Sequence Tagged Sites
Chemicals
DNA Primers DNA, Bacterial DNA, Single-Stranded T-DNA
Authors & Affiliations
28 authors, click to expand affiliations / ORCID
An Suyoung
National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea.
Park Sunhee
Jeong Dong-Hoon
Lee Dong-Yeon
Kang Hong-Gyu
Yu Jung-Hwa
Hur Junghe
Kim Sung-Ryul
Kim Young-Hea
Lee Miok
Han Soonki
Kim Soo-Jin
Yang Jungwon
Kim Eunjoo
Wi Soo Jin
Chung Hoo Sun
Hong Jong-Pil
Choe Vitnary
Lee Hak-Kyung
Choi Jung-Hee
Nam Jongmin
Kim Seong-Ryong
Park Phun-Bum
Park Ky Young
Kim Woo Taek
Choe Sunghwa
Lee Chin-Bum
An Gynheung
References (49)
49 references, click to expand
  1. Gene traps: tools for plant development and genomics.
    Plant Cell. 2000 Jul;12(7):1007-20 PMID: 10899970
  2. The plant MITE mPing is mobilized in anther culture.
    Nature. 2003 Jan 9;421(6919):167-70 PMID: 12520303
  3. Arabidopsis gene knockout: phenotypes wanted.
    Curr Opin Plant Biol. 2001 Apr;4(2):111-7 PMID: 11228432
  4. Contribution of the Tos17 retrotransposon to rice functional genomics.
    Curr Opin Plant Biol. 2001 Apr;4(2):118-22 PMID: 11228433
  5. Applications of retrotransposons as genetic tools in plant biology.
    Trends Plant Sci. 2001 Mar;6(3):127-34 PMID: 11239612
  6. The rice retrotransposon Tos17 prefers low-copy-number sequences as integration targets.
    Mol Genet Genomics. 2001 Apr;265(2):336-44 PMID: 11361345
  7. Large-scale T-DNA mutagenesis in Arabidopsis for functional genomic analysis.
    Funct Integr Genomics. 2000 May;1(1):25-34 PMID: 11793219
  8. Use of the transposon Ac as a gene-searching engine in the maize genome.
    Plant Cell. 2002 Mar;14(3):713-26 PMID: 11910016
  9. A draft sequence of the rice genome (Oryza sativa L. ssp. indica).
    Science. 2002 Apr 5;296(5565):79-92 PMID: 11935017
  10. Analysis of flanking sequences from dissociation insertion lines: a database for reverse genetics in Arabidopsis.
    Plant Cell. 1999 Dec;11(12):2263-70 PMID: 10590156
  11. T-DNA as an insertional mutagen in Arabidopsis.
    Plant Cell. 1999 Dec;11(12):2283-90 PMID: 10590158
  12. Saturation mutagenesis using maize transposons.
    Curr Opin Plant Biol. 2000 Apr;3(2):103-7 PMID: 10712955
  13. Technical advance: display and isolation of transposon-flanking sequences starting from genomic DNA or RNA.
    Plant J. 2000 Mar;21(5):495-505 PMID: 10758500
  14. Functional genomics in Arabidopsis: large-scale insertional mutagenesis complements the genome sequencing project.
    Curr Opin Biotechnol. 2000 Apr;11(2):157-61 PMID: 10753770
  15. T-DNA insertional mutagenesis for functional genomics in rice.
    Plant J. 2000 Jun;22(6):561-70 PMID: 10886776
  16. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).
    Science. 2002 Apr 5;296(5565):92-100 PMID: 11935018
  17. A collection of sequenced and mapped Ds transposon insertion sites in Arabidopsis thaliana.
    Plant Mol Biol. 2002 Sep;50(1):93-110 PMID: 12139012
  18. A new resource of locally transposed Dissociation elements for screening gene-knockout lines in silico on the Arabidopsis genome.
    Plant Physiol. 2002 Aug;129(4):1695-9 PMID: 12177482
  19. Flanking sequence tags in Arabidopsis thaliana T-DNA insertion lines: a pilot study.
    C R Biol. 2002 Jul;325(7):773-80 PMID: 12360845
  20. Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome.
    Plant J. 2002 Oct;32(2):233-42 PMID: 12383088
  21. Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes.
    Plant J. 2002 Oct;32(2):243-53 PMID: 12383089
  22. The genome sequence and structure of rice chromosome 1.
    Nature. 2002 Nov 21;420(6913):312-6 PMID: 12447438
  23. Sequence and analysis of rice chromosome 4.
    Nature. 2002 Nov 21;420(6913):316-20 PMID: 12447439
  24. A high-throughput Arabidopsis reverse genetics system.
    Plant Cell. 2002 Dec;14(12):2985-94 PMID: 12468722
  25. T-DNA insertional mutagenesis for activation tagging in rice.
    Plant Physiol. 2002 Dec;130(4):1636-44 PMID: 12481047
  26. ATIDB: Arabidopsis thaliana insertion database.
    Nucleic Acids Res. 2003 Feb 15;31(4):1245-51 PMID: 12582244
  27. In-depth view of structure, activity, and evolution of rice chromosome 10.
    Science. 2003 Jun 6;300(5625):1566-9 PMID: 12791992
  28. Genome-wide insertional mutagenesis of Arabidopsis thaliana.
    Science. 2003 Aug 1;301(5633):653-7 PMID: 12893945
  29. Transgene structures in T-DNA-inserted rice plants.
    Plant Mol Biol. 2003 Jul;52(4):761-73 PMID: 13677465
  30. Isolation of a gene encoding a novel chloroplast protein by T-DNA tagging in Arabidopsis thaliana.
    EMBO J. 1990 May;9(5):1337-46 PMID: 2158442
  31. T-DNA insertional mutagenesis in Arabidopsis.
    Plant Mol Biol. 1992 Dec;20(5):963-76 PMID: 1463832
  32. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA.
    Plant J. 1994 Aug;6(2):271-82 PMID: 7920717
  33. Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking.
    Genomics. 1995 Feb 10;25(3):674-81 PMID: 7759102
  34. Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements.
    Genes Dev. 1995 Jul 15;9(14):1797-810 PMID: 7622040
  35. Retrotransposons of rice involved in mutations induced by tissue culture.
    Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7783-8 PMID: 8755553
  36. T-DNA insertion mutagenesis in Arabidopsis: going back and forth.
    Trends Genet. 1997 Apr;13(4):152-6 PMID: 9097726
  37. Integration of T-DNA binary vector 'backbone' sequences into the tobacco genome: evidence for multiple complex patterns of integration.
    Plant J. 1997 May;11(5):945-57 PMID: 9193068
  38. In planta Agrobacterium-mediated transformation of adult Arabidopsis thaliana plants by vacuum infiltration.
    Methods Mol Biol. 1998;82:259-66 PMID: 9664431
  39. Gene identification with sequenced T-DNA tags generated by transformation of Arabidopsis cell suspension.
    Plant J. 1998 Mar;13(5):707-16 PMID: 9681013
  40. Knock-out mutants from an En-1 mutagenized Arabidopsis thaliana population generate phenylpropanoid biosynthesis phenotypes.
    Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12432-7 PMID: 9770503
  41. Strategies for cloning unknown cellular flanking DNA sequences from foreign integrants.
    Cell Mol Life Sci. 1998 Dec;54(12):1403-11 PMID: 9893713
  42. Direct repeats of T-DNA integrated in tobacco chromosome: characterization of junction regions.
    Plant J. 1998 Dec;16(6):673-80 PMID: 10069074
  43. Screening of transgenic plants by amplification of unknown genomic DNA flanking T-DNA.
    Biotechniques. 1999 Aug;27(2):308-14 PMID: 10457837
  44. Ac as a tool for the functional genomics of rice.
    Plant J. 1999 Sep;19(5):605-13 PMID: 10504582
  45. Molecular analysis of rice plants harboring an Ac/Ds transposable element-mediated gene trapping system.
    Plant J. 1999 Sep;19(5):615-23 PMID: 10504583
  46. Function search in a large transcription factor gene family in Arabidopsis: assessing the potential of reverse genetics to identify insertional mutations in R2R3 MYB genes.
    Plant Cell. 1999 Oct;11(10):1827-40 PMID: 10521515
  47. Multiple independent defective suppressor-mutator transposon insertions in Arabidopsis: a tool for functional genomics.
    Plant Cell. 1999 Oct;11(10):1841-52 PMID: 10521516
  48. A two-component enhancer-inhibitor transposon mutagenesis system for functional analysis of the Arabidopsis genome.
    Plant Cell. 1999 Oct;11(10):1853-66 PMID: 10521517
  49. Transgene repeats in aspen: molecular characterisation suggests simultaneous integration of independent T-DNAs into receptive hotspots in the host genome.
    Mol Gen Genet. 2000 Sep;264(1-2):20-8 PMID: 11016829
Article Info
Journal
Plant physiology
Abbr.
Plant Physiol
ISSN
0032-0889
DOI
10.1104/pp.103.030478
Published
2003-12-00
Epub
2003-00-20
Pages
2040-7
Language
English
Region
United States
NLM ID
0401224
PMCID
PMC300755
Subset
IM
External Links
PubMed source DOI: 10.1104/pp.103.030478 PMC Full Text View journal details
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