Transposon Insertional Mutagenesis in Rice

Methods in Molecular Biology

Volumn 678, Issue , 2011, Pages 147-177

  Upadhyaya, Narayana M ^a   Zhu, Qian Hao ^a   Bhat, Ramesh S ^b  

^a CSIRO   (Australia)

^b UNIVERSITY OF AGRICULTURAL SCIENCES   (India)

Author keywords

Flanking sequence tag; Rice; Transiently expressed transposase system; Transposons; Two component iAc Ds system

Indexed keywords

ARTICLE; GENE EXPRESSION REGULATION; GENETICS; METHODOLOGY; NORTHERN BLOTTING; RETROPOSON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RICE; SOUTHERN BLOTTING; TRANSGENIC PLANT;

BLOTTING, NORTHERN; BLOTTING, SOUTHERN; MUTAGENESIS, INSERTIONAL; ORYZA SATIVA; PLANTS, GENETICALLY MODIFIED; RETROELEMENTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

MLCS; MLOWN;

EID: 79952200528     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-682-5_12     Document Type: Chapter

References (39)

1. Hirochika, H., Guiderdoni, E., An, G., Hsing, Y. I., Eun, M. Y., Han, C. D., Upadhyaya, N., Ramachandran, S., Zhang, Q., Pereira, A., Sundaresan, V., and Leung, H. (2004) Rice mutant resources for gene discovery. Plant. Mol. Biol. 54, 325–334.
2. An, G., Lee, S., Kim, S. H., and Kim, S. R. (2005) Molecular genetics using T-DNA in rice. Plant Cell Physiol. 46, 14–22.
3. An, S., Park, S., Jeong, D. H., Lee, D. Y., Kang, H. G., Yu, J. H., Hur, J., Kim, S. R., Kim, Y. H., Lee, M., Han, S., Kim, S. J., Yang, J., Kim, E., Wi, S. J., Chung, H. S., Hong, J. P., Choe, V., Lee, H. K., Choi, J. H., Nam, J., Park, P. B., Park, K. Y., Kim, W. T., Choe, S., Lee, C. B., and An, G. (2003) Generation and analysis of end sequence database for T-DNA tagging lines in rice. Plant Physiol. 133, 2040–2047.
4. Chen, S., Jin, W., Wang, M., Zhang, F., Zhou, J., Jia, Q., Wu, Y., Liu, F., and Wu, P. (2003) Distribution and characterization of over 1000 T-DNA tags in rice genome. Plant J. 36, 105–113.
5. Sallaud, C., Gay, C., Larmande, P., Bes, M., Piffanelli, P., Piegu, B., Droc, G., Regad, F., Bourgeois, E., Meynard, D., Perin, C., Sabau, X., Ghesquiere, A., Glaszmann, J. C., Delseny, M., and Guiderdoni, E. (2004) High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics. Plant J. 39, 450–464.
6. Chin, H. G., Choe, M. S., Lee, S.-H., Park, S. H., Koo, J., Kim, N. Y., Lee, J. J., Oh, B. G., Yi, G. H., Kim, S. C., Choi, H. C., Cho, M. J., and Han, C.-D. (1999) Molecular analysis of rice plants harboring an Ac/Ds transposable element-mediated gene trapping system. Plant J. 19, 616–623.
7. Greco, R., Ouwerkerk, P. B., Taal, A. J., Sallaud, C., Guiderdoni, E., Meijer, A. H., Hoge, J. H., and Pereira, A. (2004) Transcription and somatic transposition of the maize En/Spm transposon system in rice. Mol. Genet. Genomics 270, 514–523.
8. Zhu, Q.-H., Eun, M. Y., Han, C.-D., Kumar, C. S., Pereira, A., Ramachandran, S., Sundaresan, V., Eamens, A. L., Upadhyaya, N. M., and Wu, R. (2007) Transposon insertional mutants: a resource for rice functional genomics, in Rice Functional Genomics – Challenges, Progress and Prospects (Upadhyaya, N. M., Ed.), Springer, New York, pp. 223–271.
9. Springer, P. S. (2000) Gene traps: tools for plant development and genomics. Plant Cell 12, 1007–1020.
10. Sundaresan, V., Springer, P., Volpe, T., Haward, S., Jones, J. D., Dean, C., Ma, H., and Martienssen, R. (1995) Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes Dev. 9, 1797–1810.
11. Upadhyaya, N. M., Zhu, Q. H., Zhou, X. R., Eamens, A. L., Hoque, M. S., Ramm, K., Shivakkumar, R., Smith, K. F., Pan, S. T., Li, S., Peng, K., Kim, S. J., and Dennis, E. S. (2006) Dissociation (Ds) constructs, mapped Ds launch pads and a transiently-expressed transposase system suitable for localized insertional mutagenesis in rice. Theor. Appl. Genet. 112, 1326–1341.
12. Lu, H.-J., Zhou, X.-R., Gong, Z.-X., and Upadhyaya, N. M. (2001) Generation of selectable marker-free transgenic rice using double right-border (DRB) binary vectors. Aust. J. Plant. Physiol. 28, 241–248.
13. Kumar, S. C., and Narayanan, K. K. (1997) Gene and enhancer trap constructs for isolating genetic regions from rice. Rice Biotechnol. Q. 31, 17–18.
14. Upadhyaya, N. M., Zhou, X.-R., Ramm, K., Zhu, Q.-H., Wu, L.-M., Eamens, A., Sivakumar, R., Kato, T., Yun, D.-W., Kumar, S., Narayanan, K. K., Thomas, G., Peacock, W. J., and Dennis, E. S. (2002) An iAc/Ds gene and enhancer trapping system for insertional mutagenesis in rice. Funct. Plant Biol. 29, 547–559.
15. Eamens, A. L., Blanchard, C. L., Dennis, E. S., and Upadhyaya, N. M. (2004) A bidirec- tional gene trap construct for T-DNA and Ds mediated insertional mutagenesis in rice (Oryza sativa L.). Plant Biotechnol. J. 2, 367–380.
16. Wang, M., Upadhyaya, N. M., Brettell, R. I. S., and Waterhouse, P. M. (1997) Intron-mediated improvement of a selectable marker gene for plant transformation using Agrobacterium tumefaciens. J. Genet. Breed. 51, 325–334.
17. Kolesnik, T., Szeverenyi, I., Bachmann, D., Kumar, C. S., Jiang, S., Ramamoorthy, R., Cai, M., Ma, Z. G., Sundaresan, V., and Ramachandran, S. (2004) Establishing an efficient Ac/Ds tagging system in rice: large-scale analysis of Ds flanking sequences. Plant J. 37, 301–314.
18. Chiu, W.-L., Niwa, Y., Zeng, W., Hirano, T., Kobayashi, H., and Sheen, J. (1996) Engineered GFP as a vital reporter for plants. Curr. Biol. 6, 325–330.
19. Hartley, R. W. (1988) Barnase and barstar. Expression of its cloned inhibitor permits expression of a cloned ribonuclease. J. Mol. Biol. 202, 913–915.
20. Hanahan, D. (1983) Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166, 557.
21. Lazo, G. R., Stein, P. A., and Ludwig, R. A. (1991) A DNA transformation-competent Arabidopsis genomic library in Agrobacterium. Biotechnology 9, 963–967.
22. Toki, S. (1997) Rapid and efficient Agrobacterium-meditated transformation in rice. Plant Mol. Biol. Rep. 15, 16–21.
23. Ditta, G., Stanfield, S., Corbin, D., and Helinski, D. R. (1980) Broad host range DNA cloning system for gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc. Natl. Acad. Sci. U. S. A. 77, 7347–7351.
24. Miller, J. H. (1972) Experiments in Molecular Genetics, Cold Spring Harbor Laboratory: Cold Spring Harbor, New York.
25. Thompson, J. A., Abdullah, R., and Cocking, H. (1986) Protoplast culture of rice (Oryza sativa L.) using media solidified with agarose. Plant Sci. 47, 123–133.
26. Li, L., Qu, R., Kochko, A. D., Fauquet, C., and Beachy, R. N. (1993) An improved rice transformation system using the biolistic method. Plant Cell Rep. 12, 250–255.
27. Upadhyaya, N. M., Surin, B., Schünmann, P., Ramm, K., Gaudron, J., Taylor, W. C., and Waterhouse, P. M. (2000) Agrobacterium-mediated transformation of Australian rice cultivars Jarrah and Amaroo with modified promoters and selectable markers. Aust. J. Plant. Physiol. 27, 201–210.
28. Coffman, W. R., and Herrera, R. M. (1980) Rice, in Hybridization of Crop Plants (Fehr, W. R., and Hadley, H. H., Eds.), ASA and CSSA, Madison, pp. 511–522.
29. Kurup, S., Runions, J., Kohler, U., Laplaze, L., Hodge, S., and Haseloff, J. (2005) Marking cell lineages in living tissues. Plant J. 42, 444–453.
30. Jefferson, R. A., Kavanagh, T. A., and Bevan, M. W. (1987) GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J. 6, 3901–3907.
31. Devereux, J., Haeberli, P., and Smithies, O. (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12, 387–395.
32. Liu, Y. G., Mitsukawa, N., Oosumi, T., and Whittier, R. F. (1995) Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J. 8, 457–463.
33. Helliwell, C. A., and Waterhouse, P. M. (2005) Constructs and methods for hairpin RNA-mediated gene silencing in plants. Meth. Enzymol. 392, 24–35.
34. Coen, E. S., Robbins, T. P., Almeida, J., Hudson, A., and Carpenter, R. (Eds.) (1989) Consequences and Mechanisms of Transposition in Antirrhinum majus, American Society of Microbiology, Washington DC, USA.
35. Das, L., and Martienssen, R. (1995) Site-selected transposon mutagenesis at the hcf106 locus in maize. Plant Cell 7, 287–294.
36. Gerats, A. G., Huits, H., Vrijlandt, E., Marana, C., Souer, E., and Beld, M. (1990) Molecular characterization of a nonautonomous transposable element (dTph1) of petunia. Plant Cell 2, 1121–1128.
37. Koes, R., Souer, E., van Houwelingen, A., Mur, L., Spelt, C., Quattrocchio, F., Wing, J., Oppedijk, B., Ahmed, S., Maes, T., and et al. (1995) Targeted gene inactivation in petunia by PCR-based selection of transposon insertion mutants. Proc. Natl. Acad. Sci. U. S. A. 92, 8149–8153.
38. Walbot, V. (1992) Strategies for mutagenesis and gene cloning using transposon tagging and T-DNA insertional mutagenesis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 43, 49–82.
39. Krishnan, A., Guiderdoni, E., An, G., Hsing, Y. I., Han, C. D., Lee, M. C., Yu, S. M., Upadhyaya, N., Ramachandran, S., Zhang, Q., Sundaresan, V., Hirochika, H., Leung, H., and Pereira, A. (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol. 149, 165–170.