Skip to main content
SpringerLink
Log in

Arabidopsis Genetics and Functional Genomics in the Post-genome Era

  • Chapter
Regulation of Photosynthesis

Part of the book series: Advances in Photosynthesis and Respiration ((AIPH,volume 11))

Summary

Expressed-sequence tag and genome sequencing projects for Arabidopsis and other plants have yielded unprecedented amounts of new information about plant genes. The pending completion of the genome sequences for Arabidopsis and rice will provide comprehensive knowledge of the coding capacity of higher plant genomes. It is now possible to envision assigning the specific biological functions to all genes in an angiosperm. A variety of new experimental approaches, which are enabled by large amounts of sequence information, will be used to this effect. In particular, positional cloning of Arabidopsis genes corresponding to mutations has become a standard technique. In addition, highly efficient transformation protocols for Arabidopsis make it possible to generate very large transposon and T-DNA insertion collections. Mutants for any gene can be found in these collections with minimal effort using powerful polymerase chian reaction (PCR) screening procedures or by database searches of sequenced insertion sites. New or improved methods for targeted gene disruption and large-scale gene-silencing will also be useful, particularly for understanding the function of redundant genes. Large-scale surveys of transcript, protein and metabolite levels, and collection of the results in public databases will greatly extend our knowledge of gene-expression, gene-function and regulatory networks, and will facilitate the formulation of an integrated view of the information content and processing that regulates all aspects of plant growth and development.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 379.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Aarts MGM, Dirkse WG, Stiekema WJ and Pereira A (1993) Transposon tagging of a malesterility genein Arabidopsis. Nature 363: 715–717

    Article  CAS  PubMed  Google Scholar 

  • Adams MD (1996) Serial analysis of gene expression: ESTs get smaller. Bioessays 18: 261–262

    Article  CAS  PubMed  Google Scholar 

  • Ahn S, Anderson JA, Sorrells ME and Tanksley SD (1993) Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet 241: 483–490

    Article  CAS  PubMed  Google Scholar 

  • Anderson L and Seilhamer J (1997) A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18: 533–537

    Article  CAS  PubMed  Google Scholar 

  • Avery EL, Dunstran RH and Nell JA (1998) The use of lipid metabolic profiling to assess the biological impact of marine sewage pollution. Arch Env Cont Tox 35: 229–235

    CAS  Google Scholar 

  • Avramova Z, Tikhonov A, Chen M and Bennetzen JL (1998) Matrix attachment regions and structural colinearity in the genomes of two grass species. Nucl Acids Res 26: 761–767

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  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

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Banks JF and Whitehouse CM (1996) Electrospray ionization mass spectrometry. In: Karger BL and Hancock WS (eds) Methods in Enzymology, Vol 270, pp 486–518. Academic Press, San Diego

    Google Scholar 

  • Baulcombe DC (1996) RNA as a target and an initiator of post-transcriptional gene silencing in transgenic plants. Plant Mol Biol 32: 79–88

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Beavis RC and Chait BT (1996) Matrix-assisted laser desorption ionization mass-spectrometry of proteins. In: Karger BL and Hancock WS (eds) Methods in Enzymology, Vol 270, pp 519–551. Academic Press, San Diego

    Google Scholar 

  • Bechtold N, Ellis J and Pelletier G (1993) In planta Agrobacterium-mediated gene transfer by infiltration of adult Arabidopsis thaliana plants. CR Acad Sci Paris 316: 1194–1199

    CAS  Google Scholar 

  • Beetham PR, Kipp PB, Sawycky XL, Arntzen CJ and May GD (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

    Article  CAS  PubMed  Google Scholar 

  • Bell CJ and Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19: 137–144

    Article  CAS  PubMed  Google Scholar 

  • Ben H (1999) Advances in protein solubilisation for two-dimensional electrophoresis. Electrophoresis 20: 660–663

    Google Scholar 

  • Bennetzen JL and Freeling M (1993) Grasses as a single genetic system: Genome composition, colinearity and compatibility. Trends Genet 9: 259–261

    CAS  PubMed  Google Scholar 

  • Bennetzen JL and Freeling M (1997) The unified grass genome: Synergy in synteny. Genome Res 7: 301–306

    CAS  PubMed  Google Scholar 

  • Bernard PS, Lay MJ and Wittwer CT (1998) Integrated amplification and detection of the C677T point mutation in the methylenetetrahydrofolate reductase gene by fluorescence resonance energy transfer and probemelting curves. Anal Biochem 255: 101–107

    Article  CAS  PubMed  Google Scholar 

  • Bevan M (1997) Objective: The complete sequence of a plant genome. Plant Cell 9: 476–478

    Article  CAS  PubMed  Google Scholar 

  • Bevan M, Bancroft I, Bent E, Love K, Goodman H, Dean C, Bergkamp R, Dirkse W, Van Staveren M, Stiekema W, Drost L, Ridley P, Hudson S-A, Patel K, Murphy G, Piffanelli P, Wedler H, Wedler E, Wambutt R, Weitzenegger T, Pohl TM, Terryn N, Gielen J, Villarroel R, De Clerck R, Van Montagu M, Lecharny A, Auborg S, Gy I, Kreis M, Lao N, Kavanagh T, Hempel S, Kotter P, Entian K-D, Rieger M, Schaeffer M, Funk B, Mueller-Auer S, Silvey M, James R, Montfort A, Pons A, Puigdomenech P, Douka A, Voukelatou E, Milioni D, Hatzopoulos P, Piravandi E, Obermaier B, Hilbert H, Duesterhoeft A, Moores T, Jones JDG, Eneva T, Palme K, Benes V, Rechman S, Ansorge W, Delseny M, Voet M, Volckaert G, Mewes H-W, Klosterman S, Schueller C and Chalwatzis N (1998) Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391: 485–488

    Article  CAS  PubMed  Google Scholar 

  • Bhatt AM, Page T, Lawson EJR, Lister C and Dean C (1996) Use of Ac as an insertional mutagen in Arabidopsis. Plant J 9: 935–945

    Article  CAS  PubMed  Google Scholar 

  • Blackstock WP and Weir MP (1999) Proteomics: Qualitative and physical mapping of cellular proteins. Trends Biotech 17: 121–127

    CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Bouchez D, Granier F, Bouché N, Caboche M, Bechtold N and Pelletier G (1999) T-DNA insertional mutagenesis for reverse genetics in Arabidopsis, Abstract 4-1. In: Proceedings Book of the 10th International Conference on Arabidopsis Research, University of Melbourne, Australia

    Google Scholar 

  • Brown PO and Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nature Genet 21: 33–37

    Article  CAS  PubMed  Google Scholar 

  • Bulyk ML, Gentalen E, Lockhart DJ and Church GM (1999) Quantifying DNA-protein interactions by double-stranded DNA arrays. Nature Biotech 17: 573–578

    CAS  Google Scholar 

  • Camilleri C, Lafleuriel J, Macadré C, Varoquaux F, Parmentier Y, Picard G, Caboche M and Bouchez D (1998) A YAC contig map of Arabidopsis thaliana chromosome 3. Plant J 14: 633–642

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Cardon GH, Frey M, Saedler H and Gierl A (1993) Definition and characterization of an artificial En/Spm-based transposon tagging system in transgenic tobacco. Plant Mol Biol 23: 157–178

    Article  CAS  PubMed  Google Scholar 

  • Cavell AC, Lydiate DJ, Parkin IAP, Dean C and Trick M (1998) Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome. Genome 41: 62–69

    Article  CAS  PubMed  Google Scholar 

  • Chandler VL and Hardeman KJ (1992) The Mu elements of Zea mays. Adv Genet 30: 77–122

    CAS  PubMed  Google Scholar 

  • Chang SS, Park SK, Kim BC, Kang BJ, Kim DU and Nam HG (1994) Stable genetic transformation of Arabidopsis thaliana by Agrobacterium inoculation in planta. Plant J 5: 551–558

    CAS  Google Scholar 

  • Chen M, San Miguel P, de Oliveira AC, Woo SS, Zhang H, Wing RA and Bennetzen JL (1997) Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc Natl Acad Sci USA 94: 3431–3435

    CAS  PubMed  Google Scholar 

  • Chen M, San Miguel P and Bennetzen JL (1998) Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148: 435–443

    CAS  PubMed  Google Scholar 

  • Chin HG, Choe MS, Lee SH, Park SH, Park SH, Koo JC, Kim NY, Lee JJ, Oh BG, Yi GH, Kim SC, Choi HC, Cho MJ and Han C (1999) Molecular analysis of rice plants harboring an Ac/Ds transposable element-mediated gene trapping system. Plant J 19: 615–623

    Article  CAS  PubMed  Google Scholar 

  • Cho RJ, Mindrinos M, Daniel R, Richards DR, Ronald J, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N, Theologis A, Yang W-H, Hubbell E, Au M, Chung EY, Lashkari D, Lemieux B, Dean C, Lipshutz RJ, Ausubel FM, Davis RW and Oefner PJ (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nature Genet 23: 203–207

    CAS  PubMed  Google Scholar 

  • Choi SD, Creelman R, Mullet J and Wing RA (1995) Construction and characterisation of a bacterial artificial chromosome library from Arabidopsis thaliana. Weeds World 2: 17–20

    CAS  Google Scholar 

  • Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO and Herskowitz I (1998) The transcriptional program of sporulation in budding yeast. Science 282: 699–705

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Cole-Strauss A, Yoon K, Xiang Y, Byrne BC, Rice MC, Gryn J, Holloman WK and Kmiec EB (1996) Correction of the mutation responsible for sickle cell anemia by an RNA-DNA oligonucleotide. Science 273: 1386–1389

    CAS  PubMed  Google Scholar 

  • Cooke R, Raynal M, Laudie 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

    Article  CAS  PubMed  Google Scholar 

  • Cutler S and Somerville C (1997) Cellulose synthesis: Cloning in silico. Curr Biol 7: R108–R111

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Dean C, Sjodin C, Bancroft I, Lawson E, Lister C, Scofield S and Jones J (1991) Development of an efficient transposon tagging system in Arabidopsis thaliana. Symp Soc Exp Biol 45: 63–75

    CAS  PubMed  Google Scholar 

  • Depicker A and van Montagu M (1997) Post-transcriptional gene silencing in plants. Curr Opin Cell Biol 9: 373–382

    Article  PubMed  Google Scholar 

  • DeRisi JL, Iyer VR and Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680–686

    Google Scholar 

  • DeSilva D, Reiser A, Herrmann M, Tabiti K and Wittwer C (1998) Rapid genotyping and quantification using the Light Cycler with hybridization probes. Biochemica 2: 12–15

    Google Scholar 

  • Dunn MJ and Corbett JM (1996) Two-dimensional poly-acrylamide gel electrophoresis. In: Karger BL and Hancock WS (eds) Methods in Enzymology, Vol 271, pp 177–202. Academic Press, San Diego

    Google Scholar 

  • Eisen MB and Brown PO (1999) DNA arrays for analysis of gene expression. In: Weissman S (ed) Methods in Enzymology, Vol 303, pp 179–205, Academic Press, San Diego

    Google Scholar 

  • Eisen MB, Spellman PT, Brown PO and Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863–14868

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • ESSA, European Scientists Sequencing Arabidopsis (1999) Arabidopsis chromosome IV. Abstract 3–12. In: Proceedings Book of the 10th International Conference on Arabidopsis Research, University of Melbourne, Australia

    Google Scholar 

  • Fedoroff NV, Chen F, Eckardt NA, Gomez-Buitrago AM and Raina R (1999) Global analysis of environmental stress and developmentally regulated genes in Arabidopsis. Abstract 4-4. In: Proceedings Book of the 10th International Conference on Arabidopsis Research, University of Melbourne, Australia

    Google Scholar 

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

    Article  CAS  Google Scholar 

  • Feldmann KA and Marks MD (1987) Agrobacterium-mediated transformation of germinating seeds of Arabidopsis thaliana: A non-tissue culture approach. Mol Gen Genet 208: 1–9

    Article  CAS  Google Scholar 

  • Fire A (1999) RNA-triggered gene silencing. Trends Genet 15: 358–363

    CAS  PubMed  Google Scholar 

  • Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE and Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806–811

    Article  CAS  PubMed  Google Scholar 

  • Flachmann R and Kühlbrandt W (1995) Accumulation of plant antenna complexes 1s regulated by post-transcriptional mechanisms in tobacco. Plant Cell 7: 149–160

    Article  CAS  PubMed  Google Scholar 

  • Flavell RB, Bennett MD, Smith JB and Smith DB (1974) Genome size and proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 12: 257–269

    CAS  PubMed  Google Scholar 

  • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb J-F, Dougherty BA, Merrick JM, McKenney K, Sutton G, Fitzhugh W, Fields C, Gocayne JD, Scott J, Shirley R, Liu L-I, Glodek A, Kelley JM, Weidman JF, Phillips CA, Spriggs T, Hedblom E, Cotton MD, Utterback TR, Hanna MC, Nguyen DT, Saudek DM, Brandon RC, Fine LD, Fritchman JL, Fuhrmann JL, Geoghagen NSM, Gnehm CL, McDonald LA, Small KV, Fraser CM, Smith HO and Venter JC (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 507–512

    Google Scholar 

  • Fodor SPA, Read JL, Pirrung MC, Stryer L, Lu AT and Solas D (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251: 767–773

    CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Gale MD and Devos KM (1998b) Comparative genomics in the grasses. Proc Natl Acad Sci USA 95: 1971–1974

    Article  CAS  PubMed  Google Scholar 

  • Gerhold D, Rushmore T and Caskey CT (1999) DNA chips: promising toys have become powerful tools. Trends Biochem Sci 24: 168–173

    Article  CAS  PubMed  Google Scholar 

  • Gheysen G, Herman L, Breyne P, Gielen J, Van Montagu M and Depicker A (1990) Cloning and sequence analysis of truncated T-DNA inserts from Nicotiana tabacum. Gene 94: 155–163

    Article  CAS  PubMed  Google Scholar 

  • Gibson S and Somerville C (1993) Isolating plant genes. Trends Biochem Sci 11: 306–313

    CAS  Google Scholar 

  • Gillece-Castro BL and Stults JT (1996) Peptide characterization by mass spectrometry. In: Karger BL and Hancock WS (eds) Methods in Enzymology, Vol 271, pp 427–448. Academic Press, San Diego

    Google Scholar 

  • Gilliland LU, McKinney EC, Asmussen MA and Meagher RB (1998) Detection of deleterious genotypes in multigenerational studies. I. Disruptions in individual Arabidopsis actin genes. Genetics 149: 717–725

    CAS  PubMed  Google Scholar 

  • Goff SA (1999) Rice as a model for cereal genomics. Curr Opin Plant Biol 2: 86–89

    Article  CAS  PubMed  Google Scholar 

  • Goodman HM, Ecker JR and Dean C (1995) The genome of Arabidopsis thaliana. Proc Natl Acad Sci USA 92: 10831–10835

    CAS  PubMed  Google Scholar 

  • Gruissem W (1989) Chloroplast gene expression, how plants turn their plastids on. Cell 56: 161–170

    Article  CAS  PubMed  Google Scholar 

  • Hacia JG (1999) Resequencing and mutational analysis using oligonucleotide microarrays. Nature Genet 21: 42–47

    Article  CAS  PubMed  Google Scholar 

  • Hake S and Walbot V (1980) The genome of Zea mays, its organization and homology to related grasses. Chromosoma 79: 251–270

    Article  CAS  Google Scholar 

  • Hamilton CM (1997) A binary-BAC system for plant transformation with high-molecular-weight DNA. Gene 200: 107–116

    Article  CAS  PubMed  Google Scholar 

  • Hehl R (1994) Transposon tagging in heterologous host plants. Trends Genet 10: 385–386

    Article  CAS  PubMed  Google Scholar 

  • Heller RA, Schena M, Chai A, Shalon D, Bedilion T, Gilmore J, Woolley DE and Davis RW (1997) Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci USA 94: 2150–2155

    Article  CAS  PubMed  Google Scholar 

  • Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C and Watanabe C (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci USA 93: 5011–5015

    Google Scholar 

  • Heslop Harrison JS, Murata M, Ogura Y, Schwarzacher T and Motoyoshi F (1999) Polymorphisms and genomic organization of repetitive DNA from centromeric regions of Arabidopsis chromosomes. Plant Cell 11: 31–41

    CAS  PubMed  Google Scholar 

  • Hieter P and Boguski M (1997) Functional genomics: it’s all how you read it. Science 278: 601–602

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Hofmann AH, Codon AC, Ivascu C, Russo VEA, Knight C, Cove D, Schäfer DG, Chakhparonian M and Zryd J-P (1999) A specific member of the cab multigene family can be efficiently targeted and disrupted in the moss Physcomitrella patens. Mol Gen Genet 261: 92–99

    CAS  PubMed  Google Scholar 

  • Höfte H, Desprez T, Amselem J, Chiapello H, Caboche M, Moisan A, Jourjon M-F, Charpenteau J-L, Berthomieu P, Guerrier D, Giraudat J, Quigley F, Thomas F, Yu D-Y, Mache R, Raynal M, Cooke R, Grellet F, Delseny M, Parmentier Y, de Marcillac G, Gigogt C, Fleck J, Philipps G, Axelos M, Bardet C, Tremousaygue D and Lescure B (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 

  • Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JCF, Trent JM, Staudt LM, Hudson J Jr, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO (1999) The transcriptional program in the response of human fibroplasts to serum. Science 283: 83–87

    Article  CAS  PubMed  Google Scholar 

  • Jensen ON, Wilm M, Shevchenko A and Mann M (1999) Peptide sequencing of 2-DE gel-isolated proteins by nanoelectrospray tandem mass spectrometry. Meth Mol Biol 112: 571–588

    CAS  Google Scholar 

  • Jones JDG, Carland FC, Lim 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

    Article  CAS  PubMed  Google Scholar 

  • Jungblut P and Thiede B (1997) Protein identification from 2-DE gels by MALDI mass spectrometry. Mass Spectrom Rev 16: 145–162

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Kaneko T, Katoh T, Sato S, Nakamura Y, Asamizu E, Kotani H, Miyahima N and Tabata S (1999) Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence features of the regions of 1,011,550 bp covered by seventeen P1 and TAC clones. DNA Research 6: 183–195

    Article  CAS  PubMed  Google Scholar 

  • Kehoe DM, Villand P and Somerville S (1999) Technical focus: DNA microarrays for studies of higher plants and other photosynthetic organisms. Trends Plant Sci 4: 38–41

    Article  PubMed  Google Scholar 

  • Kellogg EA (1998) Relationships of cereal crops and other grasses. Proc Natl Acad Sci USA 95: 2005–2010

    Article  CAS  PubMed  Google Scholar 

  • Kempin SA, Liljegren SJ, Block LM, Rounsley SD and Yanofsky MF (1997) Targeted disruption in Arabidopsis. Nature 389: 802–803

    Article  CAS  PubMed  Google Scholar 

  • Kinney AJ (1998) Manipulating flux through plant metabolic pathways. Curr Opin Plant Biol 1: 173–178

    Article  CAS  PubMed  Google Scholar 

  • Kjemtrup S, Sampson KS, Peele CG, Nguyen LV, Conkling MA, Thompson WF and Robertson D (1998) Gene silencing from plant DNA carried by a gemini virus. Plant J 14: 91–100

    Article  CAS  PubMed  Google Scholar 

  • Klein M, Eckert-Ossenkopp U, Schmiedeberg I, Brandt P, Unseld M, Brennicke A and Schuster W (1994) Physical mapping of the mitochondrial genome of Arabidopsis thaliana by cosmid and YAC clones. Plant J 6: 447–455

    Article  CAS  PubMed  Google Scholar 

  • Klimyuk VI, Carroll BJ, Thomas CM and Jones JDG (1993) Alkali treatment for rapid preparation of plant material for reliable PCR analysis. Technical Advance. Plant J 3: 493–494

    Article  CAS  PubMed  Google Scholar 

  • Koch KE (1996) Carbohydrate-modulated gene expression in plants. Ann Rev Plant Physiol Plant Mol Biol 47: 509–540

    CAS  Google Scholar 

  • Kohchi T, Fujishige K and Ohyama K (1995) Construction of an equalized cDNA library from Arabidopsis thaliana. Plant J 8: 771–776

    Article  CAS  PubMed  Google Scholar 

  • Komari T, Hiei Y, Ishida Y, Kumashiro T and Kubo T (1998) Advances in cereal gene transfer. Curr Opin Plant Biol 1: 161–165

    Article  CAS  PubMed  Google Scholar 

  • Koncz C, Martini N, Mayerhofer R, Koncz KZ, Koerber H, Redei GP and Schell J (1989) High-frequency T-DNA-mediated gene tagging in plants. Proc Natl Acad Sci USA 86: 8467–8471

    CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Konieczny A and Ausubel F (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4: 403–410

    Article  CAS  PubMed  Google Scholar 

  • Kotani H, Sato S, Fukami M, Hosouchi T, Nakazaki N, Okumura S, Wada T, Liu Y-G, Shibata D and Tabata S (1997) A fine physical map of Arabidopsis thaliana chromosome 5: Construction of a sequence-ready contig map. DNA Res 4: 371–378

    CAS  PubMed  Google Scholar 

  • Kren BT, Bandtopadhyay P and Steer CJ (1998) In vivo site-directed mutagenesis of the factor IX gene by chimeric RNA/DNA oligonucleotides. Nature Med 4: 285–290

    CAS  PubMed  Google Scholar 

  • Krysan PJ, Young JC, 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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Lagercrantz U (1998) Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150: 1217–1228

    CAS  PubMed  Google Scholar 

  • Lagercrantz U, Putterill J, Coupland G and Lydiate D (1996) Comparative mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time. Plant J 9: 13–20

    Article  CAS  PubMed  Google Scholar 

  • Lee NH, Weinstock KG, Kirkness EF, Earle-Hughes JA, Fuldner RA, Marmaros S, Glodek A, Gocayne JD, Adams MD, Kerlavage AR, Fraser CM and Venter JC (1995) Comparative expressed-sequence-tag analysis of differential gene expression profiles in PC-12 cells before and after nerve growth factor treatment. Proc Natl Acad Sci USA 92: 8303–8309

    CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Lin X, Kaul S, Rounsley S, Shea TP, Benito M-I, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell R, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Van Aken S, Umayam L, Tallon LK, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nioerman WC, White O, Eisen JA, Salzberg SL, Fraser CM and Venter JC (1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402: 761–768

    CAS  PubMed  Google Scholar 

  • Lipshutz RJ, Fodor SPA, Gingeras TR and Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nature Genet 21: 20–24

    Article  CAS  PubMed  Google Scholar 

  • Liu D and Crawford NM (1998) Characterization of the germinal and somatic activity of the Arabidopsis transposable element Tagl. Genetics 148: 445–456

    CAS  PubMed  Google Scholar 

  • Liu YG, Mitsukawa N, Vazquez-Tello A and Whittier RF (1995a) Generation of a high quality P1 library of Arabidopsis thaliana suitable for chromosome walking. Plant J 7: 351–358

    Article  CAS  Google Scholar 

  • Liu YG, Mitsukawa N, Oosumi T and Whittier RF (1995b) Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J 8: 457–463

    Article  CAS  PubMed  Google Scholar 

  • Liu YG, Shirano Y, Fukaki H, Yanai Y, Tasaka M, Tabata S and Shibata D (1999) Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning. Proc Natl Acad Sci USA 96: 6535–6540

    CAS  PubMed  Google Scholar 

  • Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H and Brown EL (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotech 14: 1675–1680

    Article  CAS  Google Scholar 

  • Long D and Coupland G (1998) Transposon tagging with Ac/Ds in Arabidopsis. Methods Mol Biol 82: 315–328

    CAS  PubMed  Google Scholar 

  • Lotan T, Ohto M-A, Yee KM, West MAL, Lo R, Kwong RW, Yamagishi K, Fischer RL, Goldberg RB and Harada JJ (1998) Arabidopsis LEAFY COTYLEDON 1 is sufficient to induce embryo development in vegetative cells. Cell 93: 1195–1205

    Article  CAS  PubMed  Google Scholar 

  • Ludwig SR, Bowen B, Beach L and Wessler SR (1990) A regulatory gene as a novel visible marker for maize transformation. Science 247: 449–450

    Google Scholar 

  • Lukowitz W, Gillmor CS and Scheible W-R (2000) Why it feels good to have a genome initiative working for you. Plant Physiol 123: 795–805

    Article  CAS  PubMed  Google Scholar 

  • Mandal A, Lang V, Orczyk W and Palva ET (1993) Improved efficiency for T-DNA-mediated transformation and plasmid rescue in Arabidopsis thaliana. Theor Appl Genet 86: 621–628

    Article  CAS  Google Scholar 

  • Marks MD and Feldmann KA (1989) Trichome development in Arabidopsis thaliana: I. T-DNA tagging of the GLABROUS 1 gene. Plant Cell 1: 1043–1050

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Martin W and Herrmann RG (1998) Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiol 118: 9–17

    CAS  PubMed  Google Scholar 

  • Matzke MA and Matzke AJM (1995) How and why do plants inactivate homologous (trans)genes? Plant Physiol 107: 679–685

    CAS  PubMed  Google Scholar 

  • Mayer K, Schüller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian K-D, Terryn N, Harris B, Ansorge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, Müller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Boutry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham S-A, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang Y-J, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiaens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Ramsperger U, Hilbert H, Braun M, Holzer E, Brandt A, Peters S, van Staveren M, Dirkse W, Mooijman P, Klein Lankhorst R, Rose M, Hauf J, Kötter P, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Van den Daele H, De Keyser A, Buysshaert C, Gielen J, Villarroel R, De Clercq R, Van Montagu M, Rogers J, Cronin A, Quail M, Bray-Allen S, Clark L, Doggett J, Hall S, Kay M, Lennard N, McLay K, Mayes R, Pettett A, Rajandream M-A, Lyne M, Benes V, Rechmann S, Borkova D, Blöcker H, Scharfe M, Grimm M, Löhnert T-H, Dose S, de Haan M, Maarse A, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Fartmann B, Granderath K, Dauner D, Herzl A, Neumann S, Argiriou A, Vitale D, Liguori R, Piravandi E, Massenet O, Quigley F, Clabauld G, Mündlein A, Felber R, Schnabl S, Hiller R, Schmidt W, Lecharny A, Aubourg S, Chefdor F, Cooke R, Berger C, Montfort A, Casacuberta E, Gibbons T, Weber N, Vandenbol M, Bargues M, Terol J, Torres A, Perez-Perez A, Purnelle B, Bent E, Johnson S, Tacon D, Jesse T, Heijnen L, Schwarz S, Scholler P, Heber S, Francs P, Bielke C, Frishman D, Haase D, Lemcke K, Mewes HW, Stocker S, Zaccaria P, Bevan M, Wilson RK, de la Bastide M, Habermann K, Parnell L, Dedhia N, Gnoj L, Schutz K, Huang E, Spiegel L, Sehkon M, Murray J, Sheet P, Cordes M, Abu-Threideh J, Stoneking T, Kalicki J, Graves T, Harmon G, Edwards J, Latreille P, Courtney L, Cloud J, Abbott A, Scott K, Johnson D, Minx P, Bentley D, Fulton B, Miller N, Greco T, Kemp K, Kramer J, Fulton L, Mardis E, Dante M, Pepin K, Hillier L, Nelson J, Spieth J, Ryan E, Andrews S, Geisel C, Layman D, Du H, Ali J, Berghoff A, Jones K, Drone K, Cotton M, Joshu C, Antonoiu B, Zidanic M, Strong C, Sun H, Lamar B, Yordan C, Ma P, Zhong J, Preston R, Vil D, Shekher M, Matero A, Shah R, Swaby I’K, O’Shaughnessy A, Rodriguez M, Hoffman J, Till S, Granat S, Shohdy N, Hasegawa A, Hameed A, Lodhi M, Johnson A, Chen E, Marra M, Martienssen R and McCombie WR (1999) Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402: 769–777

    CAS  PubMed  Google Scholar 

  • McKinney EC, Aali N, Traut A, Feldmann KA, Belostotsky DA, McDowell JM and Meagher RB (1995) Sequence-based identification of T-DNA insertion mutations in Arabidopsis: Actin mutants act2-1 and act4-1. Plant J 8: 613–622

    Article  CAS  PubMed  Google Scholar 

  • Meinke DW, Cherry JM, Dean C, Rounsley SD and Koornneef M (1998) Arabidopsis thaliana: A model plant for genome analysis. Science 282: 662–682

    Article  CAS  PubMed  Google Scholar 

  • Meyer K, Leube MP and Grill E (1994) A protein phosphatase 2C involved in ABA signal transduction in Arabidopsis thaliana. Science 264: 1452–1455

    CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Meyerowitz EM (1992) Introduction to the Arabidopsis genome. In: Koncz C, Chua N and Schell J (eds) Methods in Arabidopsis Research, pp 100–118. World Scientific Publishing, Singapore

    Google Scholar 

  • Meyerowitz EM (1994) Plant developmental biology: Green genes for the 21st Century. Bioessays 16: 621–625

    Article  Google Scholar 

  • Meyerowitz EM (1999) Today we have naming of parts. Nature 402: 731–732

    Article  CAS  PubMed  Google Scholar 

  • Meyerowitz EM and Somerville CR (1994) Arabidopsis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York

    Google Scholar 

  • Miao ZH and Lam E (1995) Targeted disruption of the TGA3 locus in Arabidopsis thaliana. Plant J 7: 359–365

    CAS  PubMed  Google Scholar 

  • Michaels SD and Amasino RM (1998) A robust method for detecting single-nucleotide changes as polymorphic markers by PCR. Plant J 14: 381–385

    Article  CAS  PubMed  Google Scholar 

  • Mozo T, Fischer S, Meier-Ewert S, Lehrach H and Altmann TSO (1998) Use of the IGF B AC library for physical mapping of the Arabidopsis thaliana genome. Plant J 16: 377–384

    Article  CAS  PubMed  Google Scholar 

  • Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S and Altmann T (1999) A complete BAC-based physical map of the Arabidopsis thaliana genome. Nature Genet 22: 271–275

    CAS  PubMed  Google Scholar 

  • Nacry P, Camilleri C, Courtial B, Caboche M and Bouchez D (1998) Major chromosomal rearrangements induced by T-DNA transformation in Arabidopsis. Genetics 149: 641–650

    CAS  PubMed  Google Scholar 

  • Neff MM, Neff JD, Chory J and Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: Experimental applications in Arabidopsis thaliana genetics. Plant J 14: 387–392

    Article  CAS  PubMed  Google Scholar 

  • Newman T, De Bruijn FJ, Green P, Keegstra K, Kende H, McIntosh L, Ohlrogge J, Raikhel N, Somerville S, Thomashow M, Retzel E, Somerville C (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

    Article  CAS  PubMed  Google Scholar 

  • Nuccio ML, Rhodes D, McNeil SD and Hanson AD (1999) Metabolic engineering of plants for osmotic stress resistance. Curr Opin Plant Biol 2: 128–134

    Article  CAS  PubMed  Google Scholar 

  • Ogas J, Cheng J-C, Sung ZR and Somerville C (1997) Cellular differentiation regulated by gibberellin in the Arabidopsis thaliana pickle mutant. Science 277: 91–94

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  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

    Article  CAS  PubMed  Google Scholar 

  • Parnell L, Schueller C, Zaccaria P and Mayer K (1999) The nature of the EST: Distribution across chromosome IV. Abstract 3–4. In: Proceedings Book of the 10th International Conference on Arabidopsis Research, University of Melbourne, Australia

    Google Scholar 

  • Patton WF, Steinberg TH, Berggren KN, Diwu Z and Haugland RP (1999) Combining ultrasensitive fluorescence detection with 2-D gel electrophoresis in high-throughput proteomics. FASEB J 13: A1455

    Google Scholar 

  • Pearson WR and Lipman DJ (1988) Improved tools for biological sequence comparison, Proc Natl Acad Sci USA 85: 2444–2448

    CAS  PubMed  Google Scholar 

  • Ponce MR, Robles P and Micol JL (1999) High throughput mapping in Arabidopsis thaliana. Mol Gen Genet 261: 408–415

    CAS  PubMed  Google Scholar 

  • Powell J (1998) Enhanced concatemer cloning-a modification to the SAGE (Serial Analysis of Gene Expression) technique. Nucl Acids Res 26: 3445–3446

    Article  CAS  PubMed  Google Scholar 

  • Pruitt RE and Meyerowitz EM (1986) Characterization of the genome of Arabidopsis thaliana. J Mol Biol 187: 169–183

    CAS  PubMed  Google Scholar 

  • Puchta H and Hohn B (1996) From centimorgans to base pairs — homologous recombination in plants. Trends Plant Sci 1: 340–348

    Google Scholar 

  • Rashed MS, Bucknall MP, Little D, Awad A, Jacob M, Alamoudi M, Alwattar M and Ozand PT (1997) Screening blood spots for inborn errors of metabolism by electrospray tandem mass spectrometry with a microplate batch process and a computer algorithm for automated flagging of abnormal profiles. Clin Chem 43: 1129–1141

    CAS  PubMed  Google Scholar 

  • Reinbothe S, Reinbothe C and Parthier B (1993) Methyl jasmonate-regulated translation of nuclear-encoded chloroplast proteins in barley (Hordeum vulgare L. cv. Salome). J Biol Chem 268: 10606–10611

    CAS  PubMed  Google Scholar 

  • Reski R (1998) Physcomitrella and Arabidopsis: The David and Goliath of reverse genetics. Trends Plant Sci 3: 209–210

    Article  Google Scholar 

  • Reynolds PHS (1999) Inducible gene expression in plants. CABI Publishing, New York

    Google Scholar 

  • Richmond CS, Glasner JD, Mau R, Jin H, Blattner FR (1999) Genome-wide expression profiling in Escherichia coli K-12. Nucl Acids Res 27: 3821–3835

    Article  CAS  PubMed  Google Scholar 

  • Riley J, Butler R, Ogilvie D, Finniear R, Jenner D, Powell S, Anand R, Smith JC and Markham AF (1990) A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucl Acids Res 18: 2887–2890

    CAS  PubMed  Google Scholar 

  • Rosenthal A and Jones DSC (1990) Genomic walking and sequencing by oligo-cassette mediated polymerase chain reaction. Nucl Acids Res 18: 3095–3096

    CAS  PubMed  Google Scholar 

  • Round EK, Flowers SK and Richards EJ (1997) Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure. Genome Res 11: 1045–1053

    Google Scholar 

  • Rounsley SD, Glodek A, Sutton G, Adams MD, Somerville CR, Venter JC and Kerlavage AR (1996) The construction of Arabidopsis EST assemblies: A new resource to facilitate gene identification. Plant Physiol 112: 1179–1183

    Article  Google Scholar 

  • Rounsley S, Lin X and Ketchum KA (1998) Large-scale sequencing of plant genomes. Curr Opin Plant Biol 1: 136–141

    Article  CAS  PubMed  Google Scholar 

  • Rounsley S, Subramaniam S, Cao Y, Bush D, DeLoughery C, Field C, Philipps C, Iartchouk O, Last R, Wiegand R, Fischhoff D and Timberlake B (1999) Whole genome shotgun sequencing of Arabidopsis—analysis and insight. Abstract 3–1. In: Proceedings book of the 10th International Conference on Arabidopsis Research, University of Melbourne, Australia

    Google Scholar 

  • Rouzé P, Pavy N and Rombauts S (1999) Genome annotation: which tools do we have for it? Curr Opin Plant Biol 2: 90–95

    PubMed  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: 821–833

    Article  CAS  PubMed  Google Scholar 

  • Saier MH Jr (1998) Genome sequencing and informatics: New tools for biochemical discoveries. Plant Physiol 117: 1129–1133

    Article  CAS  PubMed  Google Scholar 

  • Sankhavaram RP, Parimoo S and Weissman SM (1991) Construction of au niform abundance (normalized) cDNA library. Proc Natl Acad Sci USA 88: 1943–1947

    Google Scholar 

  • San Miguel P, Tikhonov A, Jin Y-K, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z and Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765–768

    CAS  Google Scholar 

  • Santoni V, Doumas P, Rouquie D, Mansion M, Rabilloud T and Rossignol M (1999) Large scale characterization of plant plasma membrane proteins. Biochimie 81: 655–661

    Article  CAS  PubMed  Google Scholar 

  • Sasaki T (1998) The rice genome project in Japan. Proc Natl Acad Sci USA 95: 2027–2028

    CAS  PubMed  Google Scholar 

  • Sato S, Kotani H, Hayashi R, Liu Y-G, Shibata D and Tabata S (1998) A physical map of Arabidopsis thaliana chromosome 3 represented by two contigs of CIC YAC, P1, TAC and BAC clones. DNA Res 5: 163–168

    CAS  PubMed  Google Scholar 

  • Schaefer DG and Zryd JP (1997) Efficient gene targeting in the moss Physcomitrella patens. Plant J 11: 1195–1206

    Article  CAS  PubMed  Google Scholar 

  • Schena M, Shalon D, Heller R, Chai A, Brown PO and Davis RW (1996) Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA: 10614–10619

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Schmidt R, Love K, West J, Lenehan Z and Dean C (1997) Description of 31 YAC contigs spanning the majority of Arabidopsis thaliana chromosome 5. Plant J 11: 563–573

    Article  CAS  PubMed  Google Scholar 

  • Schmidt R, Acarkan A, Boivin K, Koch M and Rossberg M (1999) Analysis of microsynteny in Arabidopsis thaliana, Brassica oleracea and Capsella rubella. Abstract 3–14. In: Proceedings Book of the 10th International Conference on Arabidopsis Research, University of Melbourne, Australia

    Google Scholar 

  • Scholl RL, Keathley DE and Baribault TJ (1981) Enhancement of root formation and fertility of shoots regenerated anther-and seedling-derived callus cultures of Arabidopsis thaliana. Z Pflanzenphysiol 104: 225–231

    CAS  Google Scholar 

  • Scholl R, Rivero L, Crist D, Ware D and Davis K (1999) Progress of ABRC in obtaining new T-DNA stocks and preparing DNA from T-DNA populations for PCR screening. Abstract 4–15. In: Proceedings Book of the 10th International Conference on Arabidopsis Research, University of Melbourne, Australia

    Google Scholar 

  • Seigneurin-Berny D, Rolland N, Garin J and Joyard J (1999) Differential extraction of hydrophobic proteins from chloroplast envelope membranes: A subcellular-specific proteomic approach to identify rare intrinsic membrane proteins. Plant J 19: 217–228

    Article  CAS  PubMed  Google Scholar 

  • Shalev G, Sitrit Y, Avivi Ragolski N, Lichtenstein C and Levy AA (1999) Stimulation of homologous recombination in plants by expression of the bacterial resolvase RuvC. Proc Natl Acad Sci USA 96: 7398–7402

    Article  CAS  PubMed  Google Scholar 

  • Shalon D, Smith SJ and Brown PO (1996) A DNA-microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 6: 639–645

    CAS  PubMed  Google Scholar 

  • Sheng J and Citovsky V (1996) Agrobacterium-plant cell DNA transport: Have virulence proteins, will travel. Plant Cell 8: 1699–1710

    Article  CAS  PubMed  Google Scholar 

  • Shevchenko A, Jensen ON, Podtelejnikov AV, Sagliocco F, Wilm M, Vorm O, Mortensen P, Shevchenko A, Boucherie H and Mann M (1996) Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels. Proc Natl Acad Sci USA 93: 14440–14445

    Article  CAS  PubMed  Google Scholar 

  • Shoemaker DD, Lashkari DA, Morris D, Mittmann M and Davis RW (1996) Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nature Genet 14: 450–456

    Article  CAS  PubMed  Google Scholar 

  • Siebert PD, Chenchik A, Kellogg DE, Lukyanov KA and Lukyanov SA (1995) An improved PCR method for walking in uncloned genomic DNA. Nucl Acids Res 23: 1087–1088

    CAS  PubMed  Google Scholar 

  • Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Cerrina F and Sussman MR (1999) Maskless fabrication of light-directed oligonucleotide microarrays using adigital micromirror array. Nature Biotech 17: 974–978

    Article  CAS  Google Scholar 

  • Smyth DR (1997) Gene silencing: Cosuppression at a distance. Curr Biol 7: R793–R795

    CAS  PubMed  Google Scholar 

  • Somerville C and Somerville S (1999) Plant functional genomics. Science 285: 380–383

    Article  CAS  PubMed  Google Scholar 

  • Spalding EP, Hirsch RE, Lewis DR, Qi Z, Sussman MR and Lewis BD (1999) Potassium uptake supporting plant growth in the absence of AKT1 channel activity: Inhibition by ammonium and stimulation by sodium. J Gen Phys 113: 909–918

    CAS  Google Scholar 

  • Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B (1998) Comprehensive identification of cellcycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273–3297

    CAS  PubMed  Google Scholar 

  • Speulman E, Metz PLJ, van Arkel G, 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

    Article  CAS  PubMed  Google Scholar 

  • Steinberg TH, Jones LJ, Haugland RP and Singer VL (1996) SYPRO orange and SYPRO red protein gel stains: One-step fluorescent staining of denaturing gels for detection of nanogram levels of protein. Anal Biochem 239: 223–237

    CAS  PubMed  Google Scholar 

  • Stitt M (1999) Nitrate regulation of metabolism and growth. Curr Opin Plant Biol 2: 178–186

    Article  CAS  PubMed  Google Scholar 

  • Stitt M and Krapp A (1999) The interaction between elevated carbon dioxide and nitrogen nutrition: the physiological and molecular background. Plant Cell Environ 22: 583–621

    Article  CAS  Google Scholar 

  • Stitt M and Sonnewald U (1995) Regulation of metabolism in transgenic plants. Annu Rev Plant Phys Plant Mol Biol 46: 341–368

    CAS  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Sutton G, White O, Adams M and Kerlavage A (1995) TIGR assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci Technol 1: 9–19

    CAS  Google Scholar 

  • Tanksley SD, Bernatzky R, Lapitan NL and Prince JP (1988) Conservation of gene repertoire but not gene order in pepper and tomato. Proc Natl Acad Sci USA 85: 6419–6423

    CAS  Google Scholar 

  • Tautz D (1989) Hypervariability of simple sequences as a general source of polymorphic DNA markers. Nucl Acids Res 17: 6463–6471

    CAS  PubMed  Google Scholar 

  • The C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012–2018

    Google Scholar 

  • Thompson HL, Schmidt R and Dean C (1996a) Analysis of the occurrence and nature of repeated DNA in an 850 kb region of Arabidopsis thaliana chromosome 4. Plant Mol Biol 32: 553–557

    Article  CAS  PubMed  Google Scholar 

  • Thompson HL, Schmidt R and Dean C (1996b) Identification and distribution of seven classes of middle-repetitive DNA in the Arabidopsis thaliana genome. Nucl Acids Res 24: 3017–3022

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  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

    Article  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

    Article  CAS  PubMed  Google Scholar 

  • Unseld M, Marienfeld JR, Brandt P and Brennicke A (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nature Genet 15: 57–61

    Article  CAS  PubMed  Google Scholar 

  • Uwer U, Willmitzer L and Altmann T (1998) Inactivation of a glycyl-tRNA synthetase leads to an arrest in plant embryo development. Plant Cell 10: 1277–1294

    Article  CAS  PubMed  Google Scholar 

  • Valvekens D, Montagu, M and Lijsebettens MV (1988) Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root explants by using kanamycin selection. Proc Natl Acad Sci USA 85: 5536–5540

    CAS  Google Scholar 

  • Van den Bulk RW, Löffler HJM, Lindhaut WH and Koornneef M (1990) Somaclonal variation in tomato: effect of explant source and a comparison with chemical mutagenesis. Theor Appl Genet 80: 817–825

    Article  Google Scholar 

  • Velculescu VE, Zhang L, Vogelstein B and Kinzler KW (1995) Serial analysis of gene expression. Science 270: 484–487

    CAS  PubMed  Google Scholar 

  • Velculescu VE, Zhang L, Zhou W, Vogelstein Jacob, Basrai MA, Bassett DE Jr, Hieter P, Vogelstein B and Kinzler KW (1997) Characterization of the yeast transcriptome. Cell 88: 243–251

    Article  CAS  PubMed  Google Scholar 

  • Voinnet O, Vain P, Angell S and Baulcombe DC (1998) Systemic spread of sequence-specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA. Cell 95: 177–187

    Article  CAS  PubMed  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

    Article  CAS  Google Scholar 

  • Walden R, Fritze H, Hayashi H, Miklashevichs E, Harling H and Schell J (1994) Activation tagging: A means of isolating genes implicated as playing a role in plant growth and development. Plant Mol Biol 26: 1521–1528

    Article  CAS  PubMed  Google Scholar 

  • Wang DG, Fan J-B, Siao C-J, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L, Stein L, Hsie L, Topaloglou T, Hubbell E, Robinson E, Mittmann M, Morris MS, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson TJ, Lipshutz R, Chee M and Lander ES (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280: 1077–1082

    CAS  PubMed  Google Scholar 

  • Waterhouse PM, Graham MW and Wang MB (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

    Article  CAS  PubMed  Google Scholar 

  • Weigel D, Ahn JH, Blázquez MA, Borevitz J, Christensen SK, Fankhauser C, Ferrándiz C, Kardailsky I, Neff MM, Nguyen JT, Sato S, Wang Z, Xia Y, Dixon RA, Harrison MJ, Lamb CJ, Yanofsky MF and Chory J (2000) Activation tagging in Arabidopsis. Plant Physiol 122: 1003–1013

    Article  CAS  PubMed  Google Scholar 

  • Weiner H (1995) Antibodies that distinguish between the serine-158 phospho-and dephospho-form of spinach leaf sucrose-phosphate synthase. Plant Physiol 108: 219–225

    CAS  PubMed  Google Scholar 

  • Wilkins MR, Williams KL, Appel RD and Hochstrasser DF (1997) Proteome Research: New Frontiers in Functional Genomics. Springer-Verlag, Berlin Heidelberg New York

    Google Scholar 

  • Winkler RG, Frank MR, Galbraight DW, Feyereisen R and Feldmann KA (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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Wodicka L, Dong H, Mittmann M, Ho M-H and Lockhart DJ (1997) Genome-wide expression monitoring in Saccharomyces cerevisiae. Nature Biotech 15: 1359–1367

    Article  CAS  Google Scholar 

  • Yamamoto K and Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35: 135–144

    Article  CAS  PubMed  Google Scholar 

  • Ye G-N, Stone D, Pang S-Z, Creely W, Gonzalez K and Hinchee M (1999) Arabidopsis ovule is the target for Agrobacterium in planta vacuum infiltration transformation. Plant J 19: 249–257

    Article  PubMed  Google Scholar 

  • Yu H, Chao J, Patek D, Mujumdar R, Mujumdar S and Waggoner AS (1994) Cyanine dye dUTP analogs for enzymatic labeling of DNA probes. Nucl Acids Res 22: 3226–3232

    CAS  PubMed  Google Scholar 

  • Zachgo EA, Wang ML, Dewdney J, Bouchez D, Camilleri C, Belmonte S, Huang L, Dolan M and Goodman HM (1996) A physical map of chromosome 2 of Arabidopsis thaliana. Genome Res 6: 19–25

    CAS  PubMed  Google Scholar 

  • Zhu T, Peterson DJ, Tagliani L, St Clair G, Baszczynski CL and Bowen B (1999) Targeted manipulation of maize genes in vivo using chimeric RNA/DNA oligonucleotides. Proc Natl Acad Sci USA 96: 8768–8773

    CAS  PubMed  Google Scholar 

  • Zupan JR and Zambryski P (1995) Transfer of T-DNA from Agrobacterium to the plant cell. Plant Physiol 107: 1041–1047

    Article  CAS  PubMed  Google Scholar 

  • Zwaal RR, Broeks A, van Meurs J, Groenin 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

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA, 94305-1297, USA

    Wolf-Rüdiger Scheible, Todd A. Richmond, Lain W. Wilson & Chris R. Somerville

Authors
  1. Wolf-Rüdiger Scheible
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Todd A. Richmond
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lain W. Wilson
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chris R. Somerville
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. University of Turku, Finland

    Eva-Mari Aro

  2. University of Stockholm/Linköping, Sweden

    Bertil Andersson

Rights and permissions

Reprints and permissions

Copyright information

© 2001 Kluwer Academic Publishers

About this chapter

Cite this chapter

Scheible, WR., Richmond, T.A., Wilson, L.W., Somerville, C.R. (2001). Arabidopsis Genetics and Functional Genomics in the Post-genome Era. In: Aro, EM., Andersson, B. (eds) Regulation of Photosynthesis. Advances in Photosynthesis and Respiration, vol 11. Springer, Dordrecht. https://doi.org/10.1007/0-306-48148-0_32

Download citation

  • DOI: https://doi.org/10.1007/0-306-48148-0_32

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-0-7923-6332-3

  • Online ISBN: 978-0-306-48148-2

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation