Journal of Plant Biology

, Volume 56, Issue 2, pp 85–90 | Cite as

Utilization of T-DNA tagging lines in rice

  • Jakyung Yi
  • Gynheung An
Original Article


We have previously developed more than 100,000 T-DNA insertion mutant populations in japonica rice. These include simple knockouts as well as those for activation tagging. T-DNA insertion sites have been determined from more than 50,000 lines. The database for insertion positions is now open to the public, and these tagging lines are widely distributed to members of the rice research community. To utilize these genetic resources more efficiently, we are summarizing the important features of these tagging vectors, rice varieties, and flanking sequences. We also provide methods for handling such materials.


Activation tagging Insertion mutagenesis Handling methods Rice T-DNA 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. An G, Watson BD, Stachel S, Gordon MP, Nester EW (1985) New cloning vehicles for transformation of higher plants. EMBO J 4:277–284PubMedGoogle Scholar
  2. An G, Ebert P, Mitra A, Ha S (1988) Binary vectors. In: Gelvin SB, Schilperoort RA (eds) Plant Molecular Biology Manual. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp A3/1–19Google Scholar
  3. An S, Park S, Jeong DH, Lee DY, Kang HG, An G (2003) Generation and analysis of end sequence database for T-DNA tagging lines in rice. Plant Physiol 133:2040–2047PubMedCrossRefGoogle Scholar
  4. Chen DH, Ronald PC (1999) A rapid DNA minipreparation method suitable for AFLP and other PCR applications. Plant Mol Biol Rep 17:53–57CrossRefGoogle Scholar
  5. Choung JI, Lee JK, Shin HT, Lee DT (1999) Growth characteristics and grain quality of different released rice varieties under nitrogen levels. Kor J Intl Agri 11:403–411Google Scholar
  6. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100PubMedCrossRefGoogle Scholar
  7. Hayashi H, Czaja I, Lubenow H, Schell J, Walden R (1992) Activation of a plant gene by T-DNA tagging: auxin-independent growth in vitro. Science 258:1350–1353PubMedCrossRefGoogle Scholar
  8. Henke W, Herdel K, Jung K, Schnorr D, Loening SA (1997) Betaine improves the PCR amplification of GC-rich DNA sequences. Nucleic Acids Res, 25:3957–3958PubMedCrossRefGoogle Scholar
  9. Jefferson RA, Kavanagh TA, Bevan MW (1987) GUS fusions: betaglucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J 6:3901–3907.PubMedGoogle Scholar
  10. Jeon JS, Lee S, Jung KH, Jun SH, Jeong DH, Lee J, Kim C, Jang S, Yang K, Nam J, An K, Han MJ, Sung RJ, Choi HS, Yu JH, Choi JH, Cho SY, Cha SS, Kim SI, An G (2000a) T-DNA insertional mutagenesis for functional genomics in rice. Plant J 22:561–570PubMedCrossRefGoogle Scholar
  11. Jeon JS, Lee S, Jung KH, Jun SH, Kim C, An G. (2000b) Tissuepreferential expression of a rice alpha-tubulin gene, OsTubA1, mediated by the first intron. Plant Physiol 123:1005–1014PubMedCrossRefGoogle Scholar
  12. Jeon J, An G (2001) Gene tagging in rice: a high throughput system for functional genomics. Plant Sci 161:211–219PubMedCrossRefGoogle Scholar
  13. Jeong DH, An S, Kang HG, Moon S, Han JJ, Park S, Lee HS, An K, An G (2002) T-DNA insertional mutagenesis for activation tagging in rice. Plant Physiol 130:1636–1644PubMedCrossRefGoogle Scholar
  14. Jeong DH, An S, Park S, Kang HG, Park GG, Kim SR, Sim J, Kim YO, Kim MK, Kim J, Shin M, Jung M, An G (2006) Generation of a flanking sequence-tag database for activation-tagging lines in japonica rice. Plant J 45:123–132PubMedCrossRefGoogle Scholar
  15. Jorgensen R, Snyder C, Jones JGD (1987) T-DNA is organized predominantly in inverted repeat structure in plants transformed with Agrobacterium tumefaciens C58 derivatives. Mol Gen Genet 207:478–485CrossRefGoogle Scholar
  16. Jung KH, Han MJ, Lee YS, Kim YW, Hwang I, Kim MJ, Kim YK, Nahm BH, An G (2005) Rice Undeveloped Tapetum1 is a major regulator of early tapetum development. Plant Cell 17:2705–2722PubMedCrossRefGoogle Scholar
  17. Jung KH, Han MJ, Lee DY, Lee YS, Schreiber L, An G (2006) Waxdeficient anther1 is involved in cuticle and wax production in rice anther walls and is required for pollen development. Plant Cell 18:3015–3032PubMedCrossRefGoogle Scholar
  18. Kim SR, Lee J, Jun SH, Park S, Kang HG, Kwon S, An G (2003) Transgene structures in T-DNA-inserted rice plants. Plant Mol Biol 52:761–773PubMedCrossRefGoogle Scholar
  19. Kim SR, Jeon JS, An G (2011) Development of an efficient inverse PCR method for isolating gene tags from T-DNA insertional mutants in rice. Meth Mol Biol 678:139–146CrossRefGoogle Scholar
  20. Lee S, Jeon JS, Jung KH, An G (1999) Binary vectors for efficinet transformation of rice. J Plant Biol 42:310–316CrossRefGoogle Scholar
  21. Lee S, Choi SC, An G (2008) Rice SVP-group MADS-box proteins, OsMADS22 and OsMADS55, are negative regulators of brassinosteroid responses. Plant J 54:93–105PubMedCrossRefGoogle Scholar
  22. Lee S, Jeon US, Lee SJ, Kim YK, Persson DP, Husted S, Schjorring JK, Kakei Y, Masuda H, Nishizawa NK, An G (2009) Iron fortification of rice seeds through activation of the nicotianamine synthase gene. Proc Natl Acad Sci USA 106:22014–22019PubMedCrossRefGoogle Scholar
  23. Lee YS, Jeong DH, Lee DY, Yi J, Ryu CH, Kim SL, Jeong HJ, Choi SC, Jin P, Yang J, Cho LH, Choi H, An G (2010) OsCOL4 is a constitutive flowering repressor upstream of Ehd1 and downstream of OsphyB. Plant J 63:18–30PubMedGoogle Scholar
  24. Lucca P, Ye XD, Potrykus I (2001) Effective selection and regeneration of transgenic rice plants with mannose as selective agent. Mol Breed 7:43–49CrossRefGoogle Scholar
  25. Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15:1771–1780PubMedCrossRefGoogle Scholar
  26. Ra DS, Han SS, Min HS, Kim CK, Ryu HY (1997) Incidences of rice blast on new rice cultivars released in 1997 and some elite lines observed at different locations and in different years in Korea. Korean J. Plant Pathol 13:79–84Google Scholar
  27. Ryu CH, You JH, Kang HG, Hur J, Kim YH, Han MJ, An K, Chung BC, Lee CH, An G (2004) Generation of T-DNA tagging lines with a bidirectional gene trap vector and the establishment of an insertion-site database. Plant Mol Biol 54:489–502PubMedCrossRefGoogle Scholar
  28. Ryu CH, Lee S, Cho LH, Kim SL, Lee YS, Choi SC, Jeong HJ, Yi J, Park SJ, Han CD, An G (2009) OsMADS50 and OsMADS56 function antagonistically in regulating long day (LD)-dependent flowering in rice. Plant Cell Environ 32:1412–1427PubMedCrossRefGoogle Scholar
  29. Tachibana K, Watanabe T, Sekizawa T, Takematsu T (1986) Action mechanism of bialaphos II: accumulation of ammonia in plants treated with bialaphos. J Pest Sci 11:33–37CrossRefGoogle Scholar
  30. Waterhouse PM, Helliwell CA (2003) Exploring plant genomes by RNA-induced gene silencing. Nat Rev Genet 4:29–38PubMedCrossRefGoogle Scholar
  31. Wu JL, Wu C, Lei C, Baraoidan M, Bordeos A, Madamba MR, Ramos-Pamplona M, Mauleon R, Portugal A, Ulat VJ, Bruskiewich R, Wang G, Leach J, Khush G, Leung H (2005) Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol Biol 59:85–97PubMedCrossRefGoogle Scholar

Copyright information

© Korean Society of Plant Biologists and Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Crop Biotech Institute and Department of Genetic EngineeringKyung Hee UniversityYonginKorea

Personalised recommendations