Establishing gene function by mutagenesis in Arabidopsis thaliana

Plant Journal

Volumn 39, Issue 5, 2004, Pages 682-696

  Østergaard, Lars ^a   Yanofsky, Martin F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Arabidopsis; Forward genetics; Functional genomics; Gene function; Mutagenesis; Reverse genetics

Indexed keywords

ALGORITHMS; BIOMARKERS; DNA; GENES; GENETIC ENGINEERING;

GENE FUNCTIONS; MOLECULAR MARKERS; MUTANTS;

MUTAGENESIS;

BACTERIAL DNA; T DNA; T-DNA;

ARABIDOPSIS; GENE; GENETICS; MUTAGENESIS; NUCLEOTIDE SEQUENCE; PHENOTYPE; POLYMERASE CHAIN REACTION; REVIEW; TRANSPOSON;

ARABIDOPSIS; BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; GENES, PLANT; MUTAGENESIS; PHENOTYPE; POLYMERASE CHAIN REACTION;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA; INSERTION SEQUENCES; TRANSPOSONS;

EID: 4544246444     PISSN: 09607412     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2004.02149.x     Document Type: Review

References (78)

1. Alonso, J.M., Stepanova, A.N., Leisse, T.J. et al. (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science, 301, 653-657.
2. Azpiroz-Leehan, R. and Feldmann, K.A. (1997) T-DNA insertion mutagenesis in Arabidopsis: going back and forth. Trends Genet. 13, 152-156.
3. Balzerque, S., Dubreucq, B., Chauvin, S. et al. (2001) Improved PCR-walking for large-scale isolation of plant T-DNA borders. Biotechniques, 30, 496-504.
4. Bechtold, N. and Pelletier, G. (1998) In planta Agrobacterium-mediated transformation of adult Arabidopsis thaliana plants by vacuum infiltration. Methods Mol. Biol. 82, 259-266.
5. Bechtold, N., Ellis, J. and Pelletier, G. (1993) In planta Agrobacterium-mediated gene transfer by infiltration of adult Arabidopsis thaliana plants. C. R. Acad. Sci. Paris, 316, 1194-1199.
6. Beetham, P.R., Kipp, P.B., Sawycky, X.L., Arntzen, C.J. and May, G.D. (1999) A tool for functional plant genomics: chimeric RNA/ DNA oligonucleotides cause in vivo gene-specific mutations. Proc. Natl Acad. Sci. USA, 96, 8774-8778.
7. Benfey, P.N., Ren, L. and Chua, N.-H. (1989) The CaMV 35S enhancer contains at least two domains which can confer different developmental and tissue-specific expression patterns. EMBO J. 8, 2195-2202.
8. Bowman, J.L., Smyth, D.R. and Meyerowitz, E.M. (1989) Genes directing flower development in Arabidopsis. Plant Cell, 1, 37-52.
9. Bowman, J.L., Smyth, D.R. and Meyerowitz, E.M. (1991) Genetic interactions among floral homeotic genes of Arabidopsis. Development, 112, 1-20.
10. Brodersen, P., Petersen, M., Pike, H.M., Olszak, B., Skov, S., Odum, N., Jorgensen, L.B., Brown, R.E. and Mundy, J. (2002) Knockout of Arabidopsis accelerated-cell-death11 encoding a sphingosine transfer protein causes activation of programmed cell death and defense. Genes Dev. 16, 490-502.
11. Brusslan, J.A., Karlin-Neumann, G.A., Huang, L. and Tobin, E.M. (1993) An Arabidopsis mutant with a reduced level of cab140 RNA is a result of cosuppression. Plant Cell, 5, 667-677.
12. 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.
13. Chory, J., Ecker, J.R., Briggs, S. et al. (2000) National Science Foundation-Sponsored Workshop Report: The 2010 Project' functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them. Plant Physiol. 123, 423-426.
14. Clough, S.J. and Bent, A.F. (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735-743.
15. Colbert, T., Till, B.J., Tompa, R., Reynolds, S., Steine, M.N., Yeung, A.T., McCallum, C.M., Comai, L. and Henikoff, S. (2001) High-throughput screening for induced point mutations. Plant Physiol. 126, 480-484.
16. Conklin, P.L., Norris, S.R., Wheeler, G.L., Williams, E.H., Smirnoff, N. and Last, R.L. (1999) Genetic evidence for the role of GDP-mannose in plant ascorbic acid (vitamin C) biosynthesis. Proc. Natl Acad. Sci. USA, 96, 4198-4203.
17. Dinneny, J.R., Yadegari, R., Fischer, R.L., Yanofsky, M.F. and Weigel, D. (2004) The role of JAGGED in shaping lateral organs. Development, 131, 1101-1110.
18. Edwards, K., Johnstone, C. and Thompson, C. (1991) A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucl. Acids Res. 19, 1349.
19. Eshed, Y., Baum, S.F. and Bowman, J.L. (1999) Distinct mechanisms promote polarity establishment in carpels of Arabidopsis. Cell, 99, 199-209.
20. Feldmann, K.A. (1991) T-DNA insertion mutagenesis in Arabidopsis: mutational spectrum. Plant J. 1, 71-82.
21. Feldmann, K.A., Malmberg, R.L. and Dean, C. (1994) Mutagenesis in Arabidopsis. In Arabidopsis (Meyerowitz, E. and Somerville, C.R., eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 137-172.
22. Goff, S.A., Ricke, D., Lan, T.H. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92-100.
23. Greene, E.A., Codomo, C.A., Taylor, N.E. et al. (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics, 164, 731-740.
24. Hayashi, H., Czaja, I., Lubenow, H., Schell, J. and Walden, R. (1992) Activation of a plant gene by T-DNA tagging: auxin-independent growth in vitro. Science, 258, 1350-1353.
25. Ichikawa, T., Nakazawa, M., Kawashima, M. et al. (2003) Sequence database of 1172 T-DNA insertion sites in Arabidopsis activation-tagging lines that showed phenotypes in T1 generation. Plant J. 36, 421-429.
26. Jander, G., Norris, S.R., Rounsley, S.D., Bush, D.F., Levin, I.M. and Last, R.L. (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol. 129, 440-450.
27. Johanson, U., West, J., Lister, C., Michaels, S., Amasino, R. and Dean, C. (2000) Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science, 290, 344-347.
28. Kamath, R.S. and Ahringer, J. (2003) Genome-wide RNAi screening in Caenorhabditis elegans. Methods, 30, 313-321.
29. Kamath, R.S., Fraser, A.G., Dong, Y. et al. (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature, 421, 231-237.
30. Kardailsky, I., Shukla, V.K., Ahn, J.H., Dagenais, N., Christensen, S.K., Nguyen, J.T., Chory, J., Harrison, M.J. and Weigel, D. (1999) Activation tagging of the floral inducer FT. Science, 286, 1962-1965.
31. Kempin, S.A., Liljegren, S.J., Block, L.M., Rounsley, S.D., Yanofsky, M.F. and Lam, E. (1997) Targeted disruption in Arabidopsis. Nature, 389, 802-803.
32. Kiegle, E., Moore, C.A., Haseloff, J., Tester, M.A. and Knight, M.R. (2000) Cell-type-specific calcium responses to drought, salt and cold in the Arabidopsis root. Plant J. 23, 267-278.
33. Konieczny, A. and Ausubel, P.M. (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 4, 403-410.
34. Krysan, P.J., Young, J.C. and Sussman, M.R. (1999) T-DNA as an insertional mutagen in Arabidopsis. Plant Cell, 11, 2283-2290.
35. Li, X., Zhang, Y., Clarke, J.D., Li, Y. and Dong, X. (1999) Identification and cloning of a negative regulator of systemic acquired resistance, SNI1, through a screen for suppressors of npr1-1. Cell, 98, 329-339.
36. Liljegren, S.J., Ditta, G.S., Eshed, Y., Savidge, B., Bowman, J.L. and Yanofsky, M.F. (2000) SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis. Nature, 404, 766-770.
37. Lister, C. and Dean, C. (1993) Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana. Plant J. 4, 745-750.
38. Liu, Y.G. and Whittier, R.F. (1995) Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics, 25, 674-681.
39. Lukowitz, W., Gillmor, C.S. and Scheible, W.R. (2000) Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you. Plant Physiol. 123, 795-805.
40. Lukowitz, W., Nickle, T.C., Meinke, D.W., Last, R.L., Conklin, P.L. and Somerville, C.R. (2001) Arabidopsis cyt1 mutants are deficient in a mannose-1-phosphate guanylyltransferase and point to a requirement of N-linked glycosylation for cellulose biosynthesis. Proc. Natl Acad. Sci. USA, 98, 2262-2267.
41. Marsch-Martinez, N., Greco, R., Van Arkel, G., Herrera-Estrella, L. and Pereira, A. (2002) Activation tagging using the En-I maize transposon system in Arabidopsis. Plant Physiol. 129, 1544-1556.
42. Martienssen, R.A. (1998) Functional genomics: probing plant gene function and expression with transposons. Proc. Natl Acad. Sci. USA, 95, 2021-2026.
43. May, S.T., Clements, D. and Bennett, M.J. (2002) Finding your knockout: reverse genetics techniques for plants. Mol. Biotechnol. 20, 209-221.
44. McCallum, C.M., Comai, L., Greene, E.A. and Henikoff, S. (2000) Targeted screening for induced mutations. Nat. Biotechnol. 18, 455-457.
45. McConnell, J.R., Emery, J., Eshed, Y., Bao, N., Bowman, J. and Barton, M.K. (2001) Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. Nature, 411, 709-713.
46. Meinke, D.W., Meinke, L.K., Showalter, T.C., Schissel, A.M., Mueller, L.A. and Tzafrir, I. (2003) A sequence-based map of Arabidopsis genes with mutant phenotypes. Plant Physiol. 131, 409-418.
47. Meyerowitz, E.M. (1987) Arabidopsis thaliana. Annu. Rev. Genet. 21, 93-111.
48. Murashige, T. and Skoog, F. (1962) A revised medium for rapid growth and bio-assay with tobacco tissue cultures. Physiol. Plant. 15, 473-497.
49. Nakazawa, M., Ichikawa, T., Ishikawa, A., Kobayashi, H., Tsuhara, Y., Kawashima, M., Suzuki, K., Muto, S. and Matsui, M. (2003) Activation tagging, a novel tool to dissect the functions of a gene family. Plant J. 34, 741-750.
50. Nataraj, A.J., Olivos-Glander, I., Kusukawa, N. and Highsmith, W.E., (1999) Single-strand conformation polymorphism and heteroduplex analysis for gel-based mutation detection. Electrophoresis, 20, 1177-1185.
51. Neff, M.M., Neff, J.D., Chory, J. and Pepper, A.E. (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J. 14, 387-392.
52. Palatnik, J.F., Allen, E., Wu, X., Schommer, C., Schwab, R., Carrington, J.C. and Weigel, D. (2003) Control of leaf morphogenesis by microRNAs. Nature, 425, 257-263.
53. Pan, X., Liu, H., Clarke, J., Jones, J., Bevan, M. and Stein, L. (2003) ATIDB: Arabidopsis thaliana insertion database. Nucl. Acids Res. 31, 1245-1251.
54. Parinov, S. and Sundaresan, V. (2000) Functional genomics in Arabidopsis: large-scale insertional mutagenesis complements the genome sequencing project. Curr. Opin. Biotechnol. 11, 157-161.
55. Parinov, S., Sevugan, M., Ye, D., Yang, W.C., Kumaran, M. and Sundaresan, V. (1999) Analysis of flanking sequences from dissociation insertion lines: a database for reverse genetics in Arabidopsis. Plant Cell, 11, 2263-2270.
56. Pelaz, S., Ditta, G.S., Baumann, E., Wisman, E. and Yanofsky, M.F. (2000) B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature, 405, 200-203.
57. Petersen, M., Brodersen, P., Naested, H. et al. (2000) Arabidopsis map kinase 4 negatively regulates systemic acquired resistance. Cell, 103, 1111-1120.
58. Redei, G.P. and Koncz, C. (1992) Classical mutagenesis. In Methods in Arabidopsis Research (Koncz, C., Chua, N.-H. and J. Schell, eds). Singapore: World Scientific, pp. 16-82.
59. Rhew, R.C., Østergaard, L., Saltzman, E.S. and Yanofsky, M.F. (2003) Genetic control of methyl halide production in Arabidopsis. Curr. Biol. 13, 1809-1813.
60. Roeder, A.M., Ferrandiz, C. and Yanofsky, M.F. (2003) The role of the REPLUMLESS homeodomain protein in patterning the Arabidopsis fruit. Curr. Biol. 13, 1630-1635.
61. Saiki, R.K., Gelfand, D.H., Stoffel, S., Scharf, S.J., Higuchi, R., Horn, G.T., Mullis, K.B. and Erlich, H.A. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science, 239, 487-491.
62. Sessions, A., Burke, E., Presting, G. et al. (2002) A high-throughput Arabidopsis reverse genetics system. Plant Cell, 14, 2985-2994.
63. Sha, Y., Li, S., Pel, Z., Luo, L., Tian, Y. and He, C. (2003) Generation and flanking sequence analysis of a rice T-DNA tagged population. Theor. Appl. Genet. 108, 306-314.
64. Speulman, E., Metz, P.L., van Arkel, G., te Lintel Hekkert, B., Stiekema, W.J. and Pereira, A. (1999) A two-component enhancer-inhibitor transposon mutagenesis system for functional analysis of the Arabidopsis genome. Plant Cell, 11, 1853-1866.
65. 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.
66. Sussman, M.R., Amasino, R.M., Young, J.C., Krysan, P.J. and Austin-Phillips, S. (2000) The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiol. 124, 1465-1467.
67. The Arabidopsis Genome Initiative (AGI). (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
68. Till, B.J., Reynolds, S.H., Greene, E.A. et al. (2003) Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res. 13, 524-530.
69. Torii, K.U., Mitsukawa, N., Oosumi, T., Matsuura, Y., Yokoyama, R., Whittier, R.F. and Komeda, Y. (1996) The Arabidopsis ERECTA gene encodes a putative receptor protein kinase with extracellular leucine-rich repeats. Plant Cell. 8, 735-746.
70. Tzafrir, I., Dickerman, A., Brazhnik, O., Nguyen, Q., McElver, J., Frye, C., Patton, D. and Meinke, D. (2003) The Arabidopsis SeedGenes project. Nucl. Acids Res. 31, 90-93.
71. Watson, J.D. and Crick, F.H. (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 171, 737-738.
72. Weigel, D. and Glazebrook, J. (2002) Arabidopsis: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
73. Weigel, D., Ahn, J.H., Blazquez, M.A. et al. (2000) Activation tagging in Arabidopsis. Plant Physiol. 122, 1003-1013.
74. Wellmer, F., Riechmann, J.L., Alves-Ferreira, M. and Meyerowitz, E.M. (2004) Genome-wide analysis of spatial gene expression in Arabidopsis flowers. Plant Cell. 16, 1314-1326.
75. Wesley, S.V., Helliwell, C.A., Smith, N.A. et al. (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J. 27, 581-590.
76. Winkler, R.G., Frank, M.R., Galbraith, D.W., Feyereisen, R. and Feldmann, K.A. (1998) Systematic reverse genetics of transfer-DNA-tagged lines of Arabidopsis. Isolation of mutations in the cytochrome p450 gene superfamily. Plant Physiol. 118, 743-750.
77. Yamada, K., Lim, J., Dale, J.M. et al. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 302, 842-846.
78. Zambryski, P. (1988) Basic processes underlying Agrobacterium-mediated DNA transfer to plant cells. Annu. Rev. Genet. 22, 1-30.