Theoretical and Applied Genetics

, Volume 108, Issue 2, pp 306–314

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

DOI: 10.1007/s00122-003-1423-9

Cite this article as:
Sha, Y., Li, S., Pei, Z. et al. Theor Appl Genet (2004) 108: 306. doi:10.1007/s00122-003-1423-9


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.

Supplementary material

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

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

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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