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A transgenic perspective on plant functional genomics

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Abstract

Transgenic crops are very much in the news due to the increasing public debate on their acceptance. In the scientific community though, transgenic plants are proving to be powerful tools to study various aspects of plant sciences. The emerging scientific revolution sparked by genomics based technologies is producing enormous amounts of DNA sequence information that, together with plant transformation methodology, is opening up new experimental opportunities for functional genomics analysis. An overview is provided here on the use of transgenic technology for the functional analysis of plant genes in model plants and a link made to their utilization in transgenic crops. In transgenic plants, insertional mutagenesis using heterologous maize transposons or Agrobacterium mediated T-DNA insertions, have been valuable tools for the identification and isolation of genes that display a mutant phenotype. To discover functions of genes that do not display phenotypes when mutated, insertion sequences have been engineered to monitor or change the expression pattern of adjacent genes. These gene detector insertions can detect adjacent promoters, enhancers or gene exons and precisely reflect the expression pattern of the tagged gene. Activation tag insertions can mis-express the adjacent gene and confer dominant phenotypes that help bridge the phenotype gap. Employment of various forms of gene silencing technology broadens the scope of recovering knockout phenotypes for genes with redundant function. All these transgenic strategies describing gene-phenotype relationships can be addressed by high throughput reverse genetics methods that will help provide functions to the genes discovered by genome sequencing. The gene functions discovered by insertional mutagenesis and silencing strategies along with expression pattern analysis will provide an integrated functional genomics perspective and offer unique applications in transgenic crops.

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References

  • Aarts MGM, Dirkse W, Stiekema WJ and Pereira A (1993) Transposon tagging of a male sterility gene in Arabidopsis. Nature 363: 715–717.

    PubMed  CAS  Google Scholar 

  • Arondel V, Lemieux B, Hwang I, Gibson S, Goodman HM and Somerville CR (1992) Map-based cloning of a gene controlling omega-3 fatty acid desaturation in Arabidopsis. Science 258: 1353–1355.

    PubMed  CAS  Google Scholar 

  • Azpiroz-Leehan R and Feldmann KA (1997). T-DNA insertion mutagenesis in Arabidopsis: going back and forth. Trends Genetics 13: 152–156.

    CAS  Google Scholar 

  • Babiychuk E, Fuangthong M, van Montague M, Inze D and Kushnir S (1997) Efficient gene tagging in Arabidopsis thaliana using a gene trap approach. Proc Natl Acad Sci USA 94: 12722–12727.

    PubMed  CAS  Google Scholar 

  • Baker B, Schell J, Lörz H and Fedoroff N (1986) Transposition of the maize controlling element ‘Activator’ in tobacco. Proc Natl Acad Sci USA 83: 4844–4848.

    PubMed  CAS  Google Scholar 

  • Baker B, Coupland G, Fedoroff N, Starlinger P and Schell J (1987) Phenotypic assay for excision of the maize controlling element Ac in tobacco. EMBO J 6: 1547–1554.

    PubMed  CAS  Google Scholar 

  • Baldwin D, Crane V and Rice D (1999) A comparison of gel-based, nylon filter and microarray techniques to detect differential RNA expression in plants. Curr Opin Plant Biol 2: 96–103.

    PubMed  CAS  Google Scholar 

  • Ballinger DG and Benzer S (1989). Targeted gene mutations in Drosophila. Proc Natl Acad Sci USA 86: 9402–9406.

    PubMed  CAS  Google Scholar 

  • Bancroft I and Dean C (1993). Transposition pattern of the maize element Ds in Arabidopsis thaliana. Genetics 134: 1221–1229.

    PubMed  CAS  Google Scholar 

  • Bancroft I, Bhatt AM, Sjodin C, Scofield S, Jones JDG and Dean C (1992) Development of an efficient two-element transposon tagging system in Arabidopsis thaliana. Mol Gen Genet 233: 449–461.

    PubMed  CAS  Google Scholar 

  • Bancroft I, Jones JDG and Dean C (1993). Heterologous transposon tagging of the DRL1 locus in Arabidopsis. Plant Cell 5: 631–638.

    PubMed  CAS  Google Scholar 

  • Baulcombe DC (1999) Fast forward genetics based on virus-induced gene silencing. Curr Opin Plant Biol 2: 109–113.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Bouchez D and Höfte H (1998) Functional genomics in plants. Plant Physiol 118: 725–732.

    PubMed  CAS  Google Scholar 

  • Brenner S, Williams SR, Vermaas EH, Storck T, Moon K, McCollum C, et al. (2000) In vitro cloning of complex mixtures of DNA on microbeads: Physical separation of differentially expressed cDNAs. Proc Natl Acad Sci USA 97: 1665–1670.

    PubMed  CAS  Google Scholar 

  • Bruce W, Folkerts O, Garnaat C, Crasta O, Roth B and Bowen B (2000) Expression profiling of the maize flavanoid pathway genes controlled by estradiol-inducible transcription factors CRC and P. Plant Cell 12: 65–80.

    CAS  Google Scholar 

  • Burn N, Grimwade R, Macdonald PB, Choi E-Y, Finberg K, Roeder GS et al. (1994) Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev 8: 1087–1105.

    Google Scholar 

  • Busch MA, Bomblies K and Weigel D (1999) Activation of a floral homeotic gene in Arabidopsis. Science 285: 585–587.

    PubMed  CAS  Google Scholar 

  • Campisi L, Yang Y, Yi Y, Heilig E, Herman B, Cassista AJ, et al. (1999) Generation of enhancer trap lines in Arabidopsis and characterization of expression patterns in the inflorescence. Plant J 17: 699–707.

    PubMed  CAS  Google Scholar 

  • Chang C, Kwok SF, Bleecker AB and Meyerowitz EM (1993) Arabidopsis ethylene-response gene ETR1: similarity of product to two-component regulators. Science 262: 539–544.

    PubMed  CAS  Google Scholar 

  • Chin HG, Choe MS, Lee S-H, Park SH, Park SH, Koo JC, et al. (1999) Molecular analysis of rice plants harboring an Ac/Ds transposable element-mediated gene trapping system. Plant J 19: 615–623.

    PubMed  CAS  Google Scholar 

  • Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, et al. (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet 23: 203–207.

    PubMed  CAS  Google Scholar 

  • Clough SJ and Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735–743.

    PubMed  CAS  Google Scholar 

  • Coen ES, Robbins TP, Almeida J, Hudson A and Carpenter R (1989) Consequences and mechanisms of transposition in Antirrhinum majus. In: Berg DE and Howe MM (eds.) Mobile DNA, (pp. 413–436) Am. Soc. Microbiol, Washington DC.

    Google Scholar 

  • Cooke R, Raynal M, Laudié M and Delseny M (1997) Identification of members of gene families in Arabidopsis thaliana by contig construction from partial cDNA sequences: 106 genes encoding 50 cytoplasmic ribosomal proteins. Plant J 11: 1127–1140.

    PubMed  CAS  Google Scholar 

  • Das L and Martienssen R (1995) Site-selected transposon mutagenesis at the hcf106 locus in maize. Plant Cell 7: 287–294.

    PubMed  CAS  Google Scholar 

  • Desprez T, Amselem J, Caboche M and Höfte H (1998) Differential gene expression in Arabidopsis monitored using cDNA arrays. Plant J 14: 643–652.

    PubMed  CAS  Google Scholar 

  • Dove A (1999) Proteomics: translating genomics into products. Nat Biotech 17: 233–236.

    CAS  Google Scholar 

  • Dubois P, Cutler S and Belzile FJ (1998) Regional insertional mutagenesis on chromosome III of Arabidopsis thaliana using the maize Ac element. Plant J 13: 141–151.

    PubMed  CAS  Google Scholar 

  • Enoki H, Izawa T, Kawahara M, Komatsu M, Koh S, Kyozuka J et al. (1999) Ac as a tool for the functional genomics of rice. Plant J 19: 605–613.

    PubMed  CAS  Google Scholar 

  • Fedoroff NV and Smith DL (1993) A versatile system for detecting transposition in Arabidopsis. Plant J 3: 273–289.

    PubMed  CAS  Google Scholar 

  • Feldmann KA (1991) T-DNA insertion mutagenesis in Arabidopsis: mutational spectrum. Plant J 1: 71–82.

    CAS  Google Scholar 

  • Gale MD and Devos KM (1998) Plant comparative genetics after 10 years. Science 282: 656–659.

    PubMed  CAS  Google Scholar 

  • Gaymard F, Pilot G, Lacombe B, Bouchez D, Bruneau D, Boucherez J, et al. (1998) Identification and disruption of a plant Shaker-like outward channel involved in K+ release into the xylem sap. Cell 94: 647–655.

    PubMed  CAS  Google Scholar 

  • Gerats AGM, Huits H, Vrijlandt E, Maraña C, Souer E and Beld M (1990) Molecular characterization of a non-autonomous transposable element (dTph1) of petunia. Plant Cell 2: 1121–1128.

    PubMed  CAS  Google Scholar 

  • Hamilton AJ, Brown S, Yuanhai H, Ishizuka M, Lowe A, Solis A-GA et al. (1998) A transgene with repeated DNA causes high frequency, post-transcriptional suppression of ACC-oxidase gene expression in tomato. Plant J 15: 737–746.

    CAS  Google Scholar 

  • Herbers K and Sonnewald U (1996) Manipulating metabolic partitioning in transgenic plants. Trends Biotech 14: 198–205.

    CAS  Google Scholar 

  • Herskowitz I (1987) Functional inactivation of genes by dominant negative mutations. Nature 329: 219–222.

    PubMed  CAS  Google Scholar 

  • Hirochika H (1997) Retrotransposons of rice: their regulation and use for genome analysis. Plant Mol Biol 35: 231–240.

    PubMed  CAS  Google Scholar 

  • Hirsch RE, Lewis BD, Spalding EP and Sussman MR (1998) A role for AKT1 potassium channel in plant nutrition. Science 280: 918–921.

    PubMed  CAS  Google Scholar 

  • Höfte H, Desperez T, Amselem J, Chiapollo H, Caboche M et al. (1993) An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J 4: 1051–1061.

    PubMed  Google Scholar 

  • Ito T, Seki M, Hayashida N, Shibata D and Shinozaki K (1999) Regional insertional mutagenesis of genes on Arabidopsis thaliana chromosome V using the Ac/Ds transposon in combination with a cDNA scanning method. Plant J 17: 433–444.

    PubMed  CAS  Google Scholar 

  • Jones DA, Thomas CM, Hammond-Kosack KE, Balint-Kurti PJ and Jones JDG (1994) Isolation of the tomato Cf-9 gene for resistance to Cladosporium fulvum by transposon tagging. Science 266: 789–793.

    PubMed  CAS  Google Scholar 

  • Jones JDG, Carland FM, Maliga P and Dooner HK (1989) Visual detection of transposition of the maize element Activator (Ac) in tobacco seedlings. Science 244: 204–207.

    CAS  Google Scholar 

  • Jones JDG, Carland FM, Lin E, Ralston E and Dooner HK (1990) Preferential transposition of the maize element Activator to linked chromosomal locations in tobacco. Plant Cell 2: 701–707

    PubMed  CAS  Google Scholar 

  • Kaiser K and Goodwin SF (1990) Site-selected transposon mutagenesis of Drosophila. Proc Natl Acad Sci USA 87: 1686–1690.

    PubMed  CAS  Google Scholar 

  • Kakimoto T (1996) CKI1, a histidine kinase homolog implicated in cytokinin signal transduction. Science 274: 982–985.

    PubMed  CAS  Google Scholar 

  • Kardailsky I, Shukla VK, Ahn JH, Dagenais N, Christensen SK, Nguyen JT, et al. (1999) Activation tagging of the floral inducer FT. Science 286: 1962–1965.

    PubMed  CAS  Google Scholar 

  • Kertbundit S, De Greve H, De Boeck F, van Montague M and Hernalsteens JP (1991) In vivo random ß-glucuronidase gene fusions in Arabidopsis thaliana. Proc Natl Acad Sci USA 88: 5212–5216.

    PubMed  CAS  Google Scholar 

  • Kobayashi Y, Kaya H, Goto K, Iwabuchi M and Araki T (1999) A pair of related genes with antagonsitic roles in mediating flowering signals. Science 286: 1960–1962.

    PubMed  CAS  Google Scholar 

  • Koes R, Souer E, van Houwelingen A, Mur L, Spelt C, Quattrocchio F, et al. (1995) Targeted gene inactivation in petunia by PCR-based selection of transposon insertion mutants. Proc Natl Acad Sci USA 92: 8149–8153.

    PubMed  CAS  Google Scholar 

  • Koncz C, Martini N, Mayerhofer R, Koncz-Kalman Zs, Körber H, Redei GP et al. (1989) High-frequency T-DNA-mediated gene tagging in plants. Proc Natl Acad Sci USA 86: 8467–8471.

    PubMed  CAS  Google Scholar 

  • Koncz C, Nemeth K, Redei GP and Schell J (1992) T-DNA insertional mutagenesis in Arabidopsis. Plant Mol Biol 20: 963–976.

    PubMed  CAS  Google Scholar 

  • Kooter JM, Matzke MA and Meyer P (1999) Listening to the silent genes: transgene silencing, gene regulation and pathogen control. Trends Plant Sci 4: 340–347.

    PubMed  Google Scholar 

  • Krysan PJ, Young JF, Tax F and Sussman MR (1996) Identification of transferred DNA insertions within Arabidopsis genes involved in signal transduction and ion transport. Proc Natl Acad Sci USA 93: 8145–8150.

    PubMed  CAS  Google Scholar 

  • Krysan PJ, Young JC and Sussman MR (1999) T-DNA as an insertional mutagen in Arabidopsis. Plant Cell 11: 2283–2290.

    PubMed  CAS  Google Scholar 

  • Lemieux B, Aharoni A and Schena M (1998) Overview of DNA chip technology. Mol Breeding 4: 277–289.

    CAS  Google Scholar 

  • Lin X, Kaul S, Rounsley S, Shea TP, Maria-Ines B et al. (1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402: 761–768.

    PubMed  CAS  Google Scholar 

  • Liu LX, Spoerke JM, Mulligan EL, Chen J, Reardon B et al. (1999) High-throughput isolation of Caenorhabditis elegans deletion mutants. Genome Res 9: 859–867.

    PubMed  CAS  Google Scholar 

  • Long D, Martin M, Sundberg E, Swinburne J, Puangsomlee P and Coupland G (1993) The maize transposable element system Ac/Ds as a mutagen in Arabidopsis: Identification of an albino mutation induced by Ds insertion. Proc Natl Acad Sci USA 90: 10370–10374.

    PubMed  CAS  Google Scholar 

  • Mahner M and Kary M (1997) What exactly are genomes, genotypes and phenotypes? And what about phenomes? J Theor Biol 186: 55–63.

    PubMed  CAS  Google Scholar 

  • Mandel MA, Bowman JL, Kempin SA, Ma H, Meyerowitz EM and Yanofsky MF (1992) Manipulation of flower structures in transgenic tobacco. Cell 71: 133–143.

    PubMed  CAS  Google Scholar 

  • Martienssen RA (1998) Functional genomics: Probing plant gene function and expression with transposons. Proc Natl Acad Sci USA 95: 2021–2026.

    PubMed  CAS  Google Scholar 

  • Masson P and Fedoroff N (1989) Mobility of the maize Suppressormutator element in transgenic tobacco cells. Proc Natl Acad Sci USA 86: 2219–2223.

    PubMed  CAS  Google Scholar 

  • Mathur J, Szabados L, Schaefer S, Grunenberg B, Lossow A, Jonas-Straube E, et al. (1998) Gene identification with sequenced T-DNA tags generated by transformation of Arabidopsis cell suspension. Plant J 13: 707–716.

    PubMed  CAS  Google Scholar 

  • Matsumura H, Nirasawa S and Terauchi R (1999) Transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE). Plant J 20: 719–726.

    PubMed  CAS  Google Scholar 

  • Mayer K, Schuller C, Wambutt R, Murphy G, Volckaert G et al. (1999) Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402: 769–777.

    PubMed  CAS  Google Scholar 

  • McKinney EC, Ali N, Traut A, Feldmann KA, Belostotsky DA, McDowell JM et al. (1995) Sequence-based identification of TDNA insertion mutations in Arabidopsis actin mutants act2-1 and act4-1. Plant J 8: 613–622.

    PubMed  CAS  Google Scholar 

  • Meissner RC, Jin H, Cominelli E, Denekamp M, Fuertes A, Greco R, et al. (1999) Function search in a large transcription factor gene family in Arabidopsis: Assessing the potential of reverse genetics to identify insertional mutations in R2R3 MYB genes. Plant Cell 11: 1827–1840.

    PubMed  CAS  Google Scholar 

  • Mewes HW, Albermann K, Bähr M, Frishman D, Gleissner A, Hani J, et al. (1997) Overview of the yeast genome. Nature 387: 7–9.

    PubMed  Google Scholar 

  • Meyer P and Saedler H (1996) Homology dependent gene silencing in plants. Ann Rev Plant Physiol Plant Mol Biol 47: 23–48.

    CAS  Google Scholar 

  • Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW and Young ND (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J 20: 317–332.

    PubMed  CAS  Google Scholar 

  • Miklos GLG and Rubin GM (1996) The role of the genome project in determining gene function: insights from model organisms. Cell 86: 521–529.

    PubMed  CAS  Google Scholar 

  • Mizukami Y, Huang H, Tudor M, Hu Y and Ma H (1995) Functional domains of the floral regulator AGAMOUS: Characterization of the DNA binding domain and analysis of dominant negative mutations. Plant Cell 8: 831–845.

    Google Scholar 

  • Mol J, Grotewold E and Koes R (1998) How genes paint flowers and seeds. Trends Plant Sci 3: 212–217.

    Google Scholar 

  • Nam YW, Penmetsa RV, Endre G, Uribe P, Kim D and Cook DR (1999) Construction of a bacterial artificial chromosome library of Medicago truncatula and identification of clones carrying ethylene-response genes. Theor Appl Genet 98: 638–646.

    CAS  Google Scholar 

  • Neff MM, Nguyen SM, Malancharuvil EJ, Fujioka S, Noguchi T, Seto H, et al. (1999) BAS1: A gene regulating brassinosteroid levels and light responsiveness in Arabidopsis. Proc Natl Acad Sci USA 96: 15316–15323.

    PubMed  CAS  Google Scholar 

  • Newman T, de Bruijn FJ, Green P, Keegstra K, Kende H, McIntosh L, et al. (1994) Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol 106: 1241–1255.

    PubMed  CAS  Google Scholar 

  • Ohlrogge J (1999) Plant metabolic engineering: are we ready for phase two? Curr Opin Plant Biol 2: 121–122.

    PubMed  CAS  Google Scholar 

  • O'Keefe DP, Tepperman JM, Dean C, Leto KJ, Erbes DL and Odell JT (1994) Plant expression of a bacterial cytochrome P450 that catalyzes activation of a sulfonylurea pro-herbicide. Plant Physiol 105: 473–482.

    PubMed  Google Scholar 

  • Osborne BI, Wirtz U and Baker B (1995) A system for insertional mutagenesis and chromosomal rearrangement using the Ds transposon and Cre-lox. Plant J 7: 687–701.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Paz-Ares J, Ghosal D and Saedler H (1990) Molecular analysis of the C1-I allele from Zea mays: A dominant mutant of the regulatory C1 locus. EMBO J 9: 315–321.

    PubMed  CAS  Google Scholar 

  • Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, et al. (1999) ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400: 256–261.

    PubMed  CAS  Google Scholar 

  • Pereira A (1998) Heterologous transposon tagging systems. In: Lindsey K (ed) Transgenic Plant Research (pp. 91–108) Harwood Academic Publishers, UK.

    Google Scholar 

  • Pereira A and Saedler H (1989) Transpositional behaviour of the maize En/Spm element in transgenic tobacco. EMBO J 8: 1315–1321.

    PubMed  CAS  Google Scholar 

  • Quackenbush J, Liang F, Holt I, Pertea G and Upton J (2000) The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nuc Acids Res 28: 141–145.

    CAS  Google Scholar 

  • Rabinowicz PD, Schutz K, Dedhia N, Yordan C, Parnell LD, Stein L, et al. (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat Genet 23: 305–308

    PubMed  CAS  Google Scholar 

  • Rounsley SD, Glodek A, Sutton G, Adams MD, Somerville CR, Venter JC et al. (1996) The construction of Arabidopsis expressed sequence tag assemblies. Plant Physiol 112: 1177–1183.

    PubMed  CAS  Google Scholar 

  • Ruan Y, Gilmore J and Conner T (1998) Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant J 15: 821–823.

    PubMed  CAS  Google Scholar 

  • Schena M, Shalon D, Davis RW and Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470.

    PubMed  CAS  Google Scholar 

  • Schmidt R, West J, Love K, Lenehan Z, Lister C, Thompson H et al. (1995) Physical map and organization of Arabidopsis thaliana chromosome 4. Science 270: 480–483

    PubMed  CAS  Google Scholar 

  • Shirasu K, Lahaye T, Tan M-W, Zhou F, Azevedo C and Schulze-Lefert P (1999) A Novel class of eukaryotic zinc-binding proteins is required for disease resistance signaling in barley and development in C. elegans. Cell 99: 355–366.

    PubMed  CAS  Google Scholar 

  • Skarnes WC (1990) Entrapment vectors: a new tool for mammalian genetics. Biotechnology 8: 827–831.

    PubMed  CAS  Google Scholar 

  • Smith DL and Fedoroff NV (1995) LRP1, a gene expressed in lateral and adventitous root primordia of Arabidopsis. Plant Cell 7: 735–745.

    PubMed  CAS  Google Scholar 

  • Solano R and Ecker JR (1998) Ethylene gas: perception, signaling and response. Curr Opin Plant Biol 1: 393–398.

    PubMed  CAS  Google Scholar 

  • Speulman E, Metz PLJ, van Arkel G, te Lintel Hekkert B, Stiekema WJ and Pereira A (1999) A two-component enhancer-inhibitor transposon mutagenesis system for functional analysis of the Arabidopsis genome. Plant Cell 11: 1853–1866.

    PubMed  CAS  Google Scholar 

  • Springer PS, McCombie WR, Sundaresan V and Martienssen RA (1995) Gene trap tagging of PROLIFERA, an essential MCM2-3-5-like gene in Arabidopsis. Science 268: 877–880.

    PubMed  CAS  Google Scholar 

  • Stuurman J, Nijkamp HJJ and van Haaren MJJ (1998) Molecular insertion-site selectivity of Ds in tomato. Plant J 14: 215–223.

    CAS  Google Scholar 

  • Sundaresan V, Springer P, Volpe T, Haward S, Jones JDG, Dean C, et al. (1995) Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes Dev 9: 1797–1810.

    PubMed  CAS  Google Scholar 

  • Swinburne J, Balcells L, Scofield SR, Jones JDG and Coupland G (1992) Elevated levels of Activator transposase mRNA are associated with high frequencies of Dissociation excision in Arabidopsis. Plant Cell 4: 583–595.

    PubMed  CAS  Google Scholar 

  • The C. elegans sequencing consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012–2018.

  • Tissier AF, Marillonnet S, Klimyuk V, Patel K, Torres MA, Murphy G et al. (1999) Multiple independent defective suppressor-mutator transposon insertions in Arabidopsis: A tool for functional genomics. Plant Cell 11: 1841–1852.

    PubMed  CAS  Google Scholar 

  • Topping JF and Lindsey K (1995) Insertional mutagenesis and promoter trapping in plants for the isolation of genes and the study of development. Transgenic Res 4: 291–305.

    CAS  Google Scholar 

  • Trethewey RN, Krotzky AJ and Willmitzer L (1999) Metabolic profiling: a Rosetta Stone for genomics. Curr Opin Plant Biol 2: 83–85.

    PubMed  CAS  Google Scholar 

  • Tsugeki R, Kochieva EZ and Fedoroff NV (1996) A transposon insertion in the Arabidopsis SSR16 gene causes an embryo-defective lethal mutation. Plant J 10: 479–489.

    PubMed  CAS  Google Scholar 

  • van Haaren MJJ and Ow DW (1993) Prospects of applying a combination of DNA transposition and site-specific recombination in plants: a strategy for gene identification and cloning. Plant Mol Biol 23: 525–533.

    PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • Waterhouse PM, Graham MW and Wang M-B (1998) Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl Acad Sci USA 95: 13959–13964.

    PubMed  CAS  Google Scholar 

  • Weigel D and Nilsson O (1995) A developmental switch sufficient for flower initiation in diverse plants. Nature 377: 495–500.

    PubMed  CAS  Google Scholar 

  • Weigel D, Ahn JH, Blazquez MA, Borevitz JO, Christensen SK, Fankhauser C et al. (2000) Activation tagging in Arabidopsis Plant Physiol 122: 1003–1013.

    PubMed  CAS  Google Scholar 

  • Wilson K, Long D, Swinburne J and Coupland G (1996) A dissociation insertion causes a semidominant mutation that increases expression of TINY, an Arabidopsis gene related to APETALA2. Plant Cell 8: 659–671.

    PubMed  CAS  Google Scholar 

  • Winkler RG, Frank MR, Galbraith DW, Feyereisen R and Feldmann KA (1998) Systematic reverse genetics of transfer-DNA-tagged lines of Arabidopsis. Plant Physiol 118: 743–750.

    PubMed  CAS  Google Scholar 

  • Wisman E, Hartmann U, Sagasser M, Baumann E, Palme K, Hahlbrock K, et al. (1998) Knock-out mutants from an En-1 mutagenized Arabidopsis thaliana population generate phenylpropanoid biosynthesis phenotypes. Proc Natl Acad Sci USA 95: 12432–12437.

    PubMed  CAS  Google Scholar 

  • Yoder JI (1990) A genetic analysis of mutations recovered from tomato following Agrobacterium-mediated transformation with the maize transposable elements Activator and Dissociation. Theor Appl Genet 79: 657–662.

    Google Scholar 

  • Zwaal RR, Broeks A, van Meurs J, Groene JTM and Plasterk RHA (1993) Target-selected gene inactivation in Caenorhabditis elegans by using a frozen transposon insertion mutant bank. Proc Natl Acad Sci USA 90: 7431–7435.

    PubMed  CAS  Google Scholar 

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    Andy Pereira

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Pereira, A. A transgenic perspective on plant functional genomics. Transgenic Res 9, 245–260 (2000). https://doi.org/10.1023/A:1008967916498

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