Theoretical and Applied Genetics

, Volume 108, Issue 2, pp 306–314 | Cite as

Generation and flanking sequence analysis of a rice T-DNA tagged population

  • Y. Sha
  • S. Li
  • Z. Pei
  • L. Luo
  • Y. Tian
  • C. HeEmail author


Insertional mutagenesis provides a rapid way to clone a mutated gene. Transfer DNA (T-DNA) of Agrobacterium tumefaciens has been proven to be a successful tool for gene discovery in Arabidopsis and rice (Oryza sativa L. ssp. japonica). Here, we report the generation of 5,200 independent T-DNA tagged rice lines. The T-DNA insertion pattern in the rice genome was investigated, and an initial database was constructed based on T-DNA flanking sequences amplified from randomly selected T-DNA tagged rice lines using Thermal Asymmetric Interlaced PCR (TAIL-PCR). Of 361 T-DNA flanking sequences, 92 showed long T-DNA integration (T-DNA together with non-T-DNA). Another 55 sequences showed complex integration of T-DNA into the rice genome. Besides direct integration, filler sequences and microhomology (one to several nucleotides of homology) were observed between the T-DNA right border and other portions of the vector pCAMBIA1301 in transgenic rice. Preferential insertion of T-DNA into protein-coding regions of the rice genome was detected. Insertion sites mapped onto rice chromosomes were scattered in the genome. Some phenotypic mutants were observed in the T1 generation of the T-DNA tagged plants. Our mutant population will be useful for studying T-DNA integration patterns and for analyzing gene function in rice.


Rice Genome Filler Sequence Illegitimate Recombination VirD2 Protein Nick Position 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We are grateful to Dr. Guo-liang Wang for critical reading of the manuscript. The work was supported by The Chinese Academy of Sciences (grant No. KXCX2-1-02-01), and The Basic Research Program (The '973' Program, grant No. TG2000016203) and High-Tech Program (The '863' Program, grant No. 2001AA225012) of the Ministry of Science and Technology of China.

Supplementary material

Table 1: T-DNA flanking sequences with similarity to sequences deposited in public databases

esm.pdf (205 kb)
(PDF 738 KB)


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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  1. 1.Laboratory of Plant Biotechnology, Institute of MicrobiologyThe Chinese Academy of SciencesBeijingP.R. China

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