Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you

Plant Physiology

Volumn 123, Issue 3, 2000, Pages 795-805

  Lukowitz, Wolfgang ^a   Gillmor, C Stewart ^a,b   Scheible, Wolf Rüdiger ^a  

^a GEOPHYSICAL LABORATORY   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; GENETIC MARKER; GENETIC POLYMORPHISM; MOLECULAR CLONING; POLYMERASE CHAIN REACTION; POSITIONAL CLONING;

ARABIDOPSIS; EMBRYOPHYTA;

EID: 0033926906     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.123.3.795     Document Type: Article

References (49)

1. Alonso-Blanco C, Koornneef M (2000) Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics. Trends Plant Sci 5: 22-29
2. Bell CJ, Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19: 137-144
3. Busch M, Mayer U, Jürgens G (1996) Molecular analysis of the Arabidopsis pattern formation gene GNOM: gene structure and intragenic complementation. Mol Gen Genet 250: 681-691
4. Chang C, Bowman JL, DeJohn AW, Lander ES, Meyerowitz EM (1988) Restriction fragment length polymorphism linkage map for Arabidopsis thaliana, Proc Natl Acad Sci USA 85: 6856-6860
5. Chen R, Hilson P, Sedbrook J, Rosen E, Caspar T, Masson PH (1998) The Arabidopsis thaliana AGRAVITROPIC 1 gene encodes a component of the polar-auxin-transport efflux carrier. Proc Natl Acad Sci USA 95: 15112-15117
6. Cho RJ, Mindrinos M, Richards DR, 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, Oefner PJ (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet 23: 203-207
7. Copenhaver GP, Browne WE, Preuss D (1998) Assaying genome-wide recombination and centromere functions with Arabidopsis tetrads. Proc Natl Acad Sci USA 95: 247-252
8. Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S, Lin XY, Bevan M, Murphy G, Harris B, Parnell LD, McCombie WR, Martienssen RA, Marra M, Preuss D (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286: 2468-2474
9. Feldmann KA (1991) T-DNA insertional mutagenesis in Arabidopsis: mutational spectrum. Plant J 1: 71-82
10. Hardtke CS, Berleth T (1998) The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO J 17: 1405-1411
11. Hardtke CS, Müller J, Berleth T (1996) Genetic similarity among Arabidopsis thaliana ecotypes estimated by DNA sequence comparison. Plant Mol Biol 32: 915-922
12. Hauser M-T, Adhami F, Dorner M, Fuchs E, Glössl J (1998) Generation of co-dominant PCR-based markers by duplex analysis on high-resolution gels. Plant J 16: 117-125
13. Jacobson SE, Meyerowitz EM (1997) Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277: 1100-1103
14. Klimyuk VI, Carroll BJ, Thomas CM, Jones JDG (1993) Alkali treatment for rapid preparation of plant material for reliable PCR analysis: technical advance. Plant J 3: 493-494
15. Konieczny A, Ausubel F (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4: 403-410
16. Laufs P, Autran D, Traas J (1999) A chromosomal paracentric inversion associated with T-DNA integration in Arabidopsis. Plant J 18: 131-139
17. Leung J, Bouvier-Durand M, Morris P-C, Guerrier D, Chefdor F, Giraudat J (1994) Arabidopsis ABA response gene ABI1: features of a calcium-modulated protein phosphatase. Science 264: 1448-1452
18. Li J, Chory J (1997) A putative leucine-rich repeat receptor kinase involved in brassinosteroid signal transduction. Cell 90: 929-938
19. Lin X, Kaul S, Rounsley S, Shea TP, Benito M-I, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Van Aken S, Umayam L, Talion LJ, Gill JE, Venter JC (1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402: 761-768
20. Lister C, Dean C (1993) Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana. Plant J 4: 745-750
21. Liu YG, Shirano Y, Fukaki H, Yanai Y, Tasaka M, Tabata S, 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
22. Lukowitz W, Meyer U, Jürgens G (1996) Cytokinesis in the Arabidopsis embryo involves the syntaxin-related KNOLLE gene product. Cell 84: 61-71
23. 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, (1999) Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402: 769-777
24. Mayer KFX, Schoof H, Häcker A, Lenhard M, Jürgens G, Laux T (1998) Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem. Cell 95: 805-815
25. Meinke DW, Cherry JM, Dean C, Rounsley SD, Koornneef M (1998) Arabidopsis thaliana: a model plant for genome analysis. Science 282: 662-682
26. Meyer K, Leube MP, Grill E (1994) A protein phosphatase 2C involved in ABA signal transduction in Arabidopsis thaliana. Science 264: 1452-1455
27. Michaels SD, Amasino RM (1998) A robust method for detecting single-nucleotide changes as polymorphic markers by PCR. Plant J 14: 381-385
28. Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88: 9828-9832
29. Moussian B, Schoof H, Häcker A, Jürgens G, Laux T (1998) Role of the ZWILLE gene in the regulation of central shoot meristem cell fate during Arabidopsis embryogenesis. EMBO J 17: 1799-1809
30. Murray MG, Thompson WF (1980) Rapid isolation of high-molecular-weight plant DNA. Nucleic Acids Res 8: 4321-4325
31. Nacry P, Camillieri C, Courtial B, Caboche M, Bouchez D (1998) Major chromosomal rearrangements induced by T-DNA transformation in Arabidopsis. Genetics 149: 641-650
32. Nataraj AJ, Olivos-Glander I, Kusukawa N, Highsmith WE (1999) Single-strand conformation polymorphism and heteroduplex analysis for gel-based mutation detection. Electrophoresis 20: 1177-1185
33. Neff MM, Neff JD, Chory J, 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
34. O'Donovan M, Oefner PJ, Roberts SC, Austin J, Hoogendoorn B, Guy C, Speight G, Upadhyaya M, Sommer SS, McGuffin P (1998) Blind analysis of denaturing high-performance liquid chromatography as a tool for mutation detection. Genomics 52: 44-49
35. Ogas J, Kaufmann S, Henderson J, Somerville C (1999) PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis. Proc Natl Acad Sci USA 96: 13839-13844
36. Parinov S, Sevugan M, Ye D, Yang W-C, Kumaran M, Sundaresan V (1999) Analysis of flanking sequences from Dissociation insertion lines: a database for reverse genetics in Arabidopsis. Plant Cell 11: 2263-2270
37. Ponce MR, Robles P, Micol JL (1999) High-throughput mapping in Arabidopsis thaliana. Mol Gen Genet 261: 408-415
38. Putterill J, Robson F, Lee K, Coupland G (1993) Chromosome walking with YAC clones in Arabidopsis: isolation of 1700 kb of contiguous DNA on chromosome 5, including a 300 kb region containing the flowering-time gene CO. Mol Gen Genet 239: 145-157
39. Rounsley S, Subramaniam S, Cao Y, Bush D, DeLoughery C, Field C, Phillips C, Iartchouk O, Last R, Wiegand R, Fischhoff D, Timberlake B (1999) Whole genome shotgun sequencing of Arabidopsis: analysis and insight (abstract 3-1). Proceedings of the 10th International Conference on Arabidopsis Research, July 4-8, 1999, University of Melbourne, Australia
40. Ryals J, Weymann K, Lawton K, Friedrich L, Ellis D, Steiner HY, Johnson J, Delaney TP, Jesse T, Vos P, Uknes S (1997) The Arabidopsis NIM1 protein shows homology to the mammalian transcription factor inhibitor I κ B. Plant Cell 9: 425-439
41. Sakai H, Medrano LJ, Meyerowitz EM (1995) Role of SUPERMAN in maintaining Arabidopsis floral whorl boundaries. Nature 378: 199-203
42. Shirley BW, Hanley S, Goodman HM (1992) Effects of ionizing radiation on a plant genome: analysis of two Arabidopsis transparent-testa mutations. Plant Cell 4: 333-347
43. Speulman E, Metz PLJ, van Arkel G, Hekkert BTL, Stiekema WJ, Pereia A (1999) A two-component Enhancer-Inhibitor transposon mutagenesis system for functional analysis of the Arabidopsis genome. Plant Cell 11: 1853-1866
44. Tautz D (1989) Hypervariability of simple sequences as a general source of polymorphic DNA markers. Nucleic Acids Res 17: 6463-6471
45. Taylor GR (1999) Enzymatical and chemical cleaving methods. Electrophoresis 20: 1125-1130
46. Tissier AF, Marillonnet S, Klimyuk V, Patel K, Torres MA, Murphy G, Jones JDG (1999) Multiple independent defective Suppressor-mutator transposon insertions in Arabidopsis: a tool for functional genomics. Plant Cell 11: 1841-1852
47. Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Homes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407-4414
48. Wolffe AP, Matzke MA (1999) Epigenetics: regulation through repression. Science 286: 481-486
49. Zhong R, Ye Z-H (1999) IFL1, a gene regulating interfascicular fiber differentiation in Arabidopsis, encodes a homeodomain-leucine zipper protein. Plant Cell 11: 2139-2152