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Plant Physiol, June 2002, Vol. 129, pp. 440-450

Arabidopsis Map-Based Cloning in the Post-Genome Era

Georg Jander,* Susan R. Norris, Steven D. Rounsley, David F. Bush, Irena M. Levin,1 and Robert L. Last

Cereon Genomics LLC, 45 Sidney Street, Cambridge, Massachusetts 02139

Map-based cloning is an iterative approach that identifies the underlying genetic cause of a mutant phenotype. The major strength of this approach is the ability to tap into a nearly unlimited resource of natural and induced genetic variation without prior assumptions or knowledge of specific genes. One begins with an interesting mutant and allows plant biology to reveal what gene or genes are involved. Three major advances in the past 2 years have made map-based cloning in Arabidopsis fairly routine: sequencing of the Arabidopsis genome, the availability of more than 50,000 markers in the Cereon Arabidopsis Polymorphism Collection, and improvements in the methods used for detecting DNA polymorphisms. Here, we describe the Cereon Collection and show how it can be used in a generic approach to mutation mapping in Arabidopsis. We present the map-based cloning of the VTC2 gene as a specific example of this approach.


1 Present address: Syrrx Inc., 10410 Science Center Drive, San Diego, CA 92121.

* Corresponding author; e-mail georg.jander{at}cereon.com; fax 617-551-1950.

© 2002 American Society of Plant Physiologists



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J Exp BotHome page
H.-C. Jing, J. H. M. Schippers, J. Hille, and P. P. Dijkwel
Ethylene-induced leaf senescence depends on age-related changes and OLD genes in Arabidopsis
J. Exp. Bot., November 1, 2005; 56(421): 2915 - 2923.
[Abstract] [Full Text] [PDF]


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GENES CELLSHome page
K. Onai and M. Ishiura
PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock
Genes Cells, October 1, 2005; 10(10): 963 - 972.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
N. Suetsugu, T. Kagawa, and M. Wada
An Auxilin-Like J-Domain Protein, JAC1, Regulates Phototropin-Mediated Chloroplast Movement in Arabidopsis
Plant Physiology, September 1, 2005; 139(1): 151 - 162.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
J. Forner, B. Weber, C. Wietholter, R. C. Meyer, and S. Binder
Distant sequences determine 5' end formation of cox3 transcripts in Arabidopsis thaliana ecotype C24
Nucleic Acids Res., August 17, 2005; 33(15): 4673 - 4682.
[Abstract] [Full Text] [PDF]


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GeneticsHome page
J. M. Cork and M. D. Purugganan
High-Diversity Genes in the Arabidopsis Genome
Genetics, August 1, 2005; 170(4): 1897 - 1911.
[Abstract] [Full Text] [PDF]


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Plant CellHome page
N. K. Clay and T. Nelson
The Recessive Epigenetic swellmap Mutation Affects the Expression of Two Step II Splicing Factors Required for the Transcription of the Cell Proliferation Gene STRUWWELPETER and for the Timing of Cell Cycle Arrest in the Arabidopsis Leaf
PLANT CELL, July 1, 2005; 17(7): 1994 - 2008.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
N. K. Clay and T. Nelson
Arabidopsis thickvein Mutation Affects Vein Thickness and Organ Vascularization, and Resides in a Provascular Cell-Specific Spermine Synthase Involved in Vein Definition and in Polar Auxin Transport
Plant Physiology, June 1, 2005; 138(2): 767 - 777.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
S. P. Hazen, J. O. Borevitz, F. G. Harmon, J. L. Pruneda-Paz, T. F. Schultz, M. J. Yanovsky, S. J. Liljegren, J. R. Ecker, and S. A. Kay
Rapid Array Mapping of Circadian Clock and Developmental Mutations in Arabidopsis
Plant Physiology, June 1, 2005; 138(2): 990 - 997.
[Abstract] [Full Text] [PDF]


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GeneticsHome page
K. D. Edwards, J. R. Lynn, P. Gyula, F. Nagy, and A. J. Millar
Natural Allelic Variation in the Temperature-Compensation Mechanisms of the Arabidopsis thaliana Circadian Clock
Genetics, May 1, 2005; 170(1): 387 - 400.
[Abstract] [Full Text] [PDF]


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Plant CellHome page
Y. Zhang and X. Li
A Putative Nucleoporin 96 Is Required for Both Basal Defense and Constitutive Resistance Responses Mediated by suppressor of npr1-1,constitutive 1
PLANT CELL, April 1, 2005; 17(4): 1306 - 1316.
[Abstract] [Full Text] [PDF]


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Plant CellHome page
K. A. Green, M. J. Prigge, R. B. Katzman, and S. E. Clark
CORONA, a Member of the Class III Homeodomain Leucine Zipper Gene Family in Arabidopsis, Regulates Stem Cell Specification and Organogenesis
PLANT CELL, March 1, 2005; 17(3): 691 - 704.
[Abstract] [Full Text] [PDF]


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Plant CellHome page
S. Mochizuki, A. Harada, S. Inada, K. Sugimoto-Shirasu, N. Stacey, T. Wada, S. Ishiguro, K. Okada, and T. Sakai
The Arabidopsis WAVY GROWTH 2 Protein Modulates Root Bending in Response to Environmental Stimuli
PLANT CELL, February 1, 2005; 17(2): 537 - 547.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
S. Rudd, H. Schoof, and K. Mayer
PlantMarkers--a database of predicted molecular markers from plants
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D628 - D632.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
R. A. Silady, T. Kato, W. Lukowitz, P. Sieber, M. Tasaka, and C. R. Somerville
The gravitropism defective 2 Mutants of Arabidopsis Are Deficient in a Protein Implicated in Endocytosis in Caenorhabditis elegans
Plant Physiology, October 1, 2004; 136(2): 3095 - 3103.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
D. H. Hobbs, J. E. Flintham, and M. J. Hills
Genetic Control of Storage Oil Synthesis in Seeds of Arabidopsis
Plant Physiology, October 1, 2004; 136(2): 3341 - 3349.
[Abstract] [Full Text] [PDF]


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Genome ResHome page
F. A. Feltus, J. Wan, S. R. Schulze, J. C. Estill, N. Jiang, and A. H. Paterson
An SNP Resource for Rice Genetics and Breeding Based on Subspecies Indica and Japonica Genome Alignments
Genome Res., September 1, 2004; 14(9): 1812 - 1819.
[Abstract] [Full Text] [PDF]


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Plant CellHome page
L. Ball, G.-P. Accotto, U. Bechtold, G. Creissen, D. Funck, A. Jimenez, B. Kular, N. Leyland, J. Mejia-Carranza, H. Reynolds, et al.
Evidence for a Direct Link between Glutathione Biosynthesis and Stress Defense Gene Expression in Arabidopsis
PLANT CELL, September 1, 2004; 16(9): 2448 - 2462.
[Abstract] [Full Text] [PDF]


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Proc. Natl. Acad. Sci. USAHome page
S. Park and S. R. Rodermel
Mutations in ClpC2/Hsp100 suppress the requirement for FtsH in thylakoid membrane biogenesis
PNAS, August 24, 2004; 101(34): 12765 - 12770.
[Abstract] [Full Text] [PDF]


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Plant CellHome page
H.-w. Chuang, W. Zhang, and W. M. Gray
Arabidopsis ETA2, an Apparent Ortholog of the Human Cullin-Interacting Protein CAND1, Is Required for Auxin Responses Mediated by the SCFTIR1 Ubiquitin Ligase
PLANT CELL, July 1, 2004; 16(7): 1883 - 1897.
[Abstract] [Full Text] [PDF]


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Plant CellHome page
R. Ahlfors, S. Lang, K. Overmyer, P. Jaspers, M. Brosche, A. Tauriainen, H. Kollist, H. Tuominen, E. Belles-Boix, M. Piippo, et al.
Arabidopsis RADICAL-INDUCED CELL DEATH1 Belongs to the WWE Protein-Protein Interaction Domain Protein Family and Modulates Abscisic Acid, Ethylene, and Methyl Jasmonate Responses
PLANT CELL, July 1, 2004; 16(7): 1925 - 1937.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
Y.-J. Shen, H. Jiang, J.-P. Jin, Z.-B. Zhang, B. Xi, Y.-Y. He, G. Wang, C. Wang, L. Qian, X. Li, et al.
Development of Genome-Wide DNA Polymorphism Database for Map-Based Cloning of Rice Genes
Plant Physiology, July 1, 2004; 135(3): 1198 - 1205.
[Abstract] [Full Text] [PDF]


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DevelopmentHome page
A.-E. Guitton, D. R. Page, P. Chambrier, C. Lionnet, J.-E. Faure, U. Grossniklaus, and F. Berger
Identification of new members of Fertilisation Independent Seed Polycomb Group pathway involved in the control of seed development in Arabidopsis thaliana
Development, June 15, 2004; 131(12): 2971 - 2981.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
W.A. Rensink and C. R. Buell
Arabidopsis to Rice. Applying Knowledge from a Weed to Enhance Our Understanding of a Crop Species
Plant Physiology, June 1, 2004; 135(2): 622 - 629.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
E. J.M. Clerkx, M. E. El-Lithy, E. Vierling, G. J. Ruys, H. Blankestijn-De Vries, S. P.C. Groot, D. Vreugdenhil, and M. Koornneef
Analysis of Natural Allelic Variation of Arabidopsis Seed Germination and Seed Longevity Traits between the Accessions Landsberg erecta and Shakdara, Using a New Recombinant Inbred Line Population
Plant Physiology, May 1, 2004; 135(1): 432 - 443.
[Abstract] [Full Text] [PDF]


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Proc. Natl. Acad. Sci. USAHome page
D. R. Page, C. Kohler, J. A. da Costa-Nunes, C. Baroux, J. M. Moore, and U. Grossniklaus
Intrachromosomal excision of a hybrid Ds element induces large genomic deletions in Arabidopsis
PNAS, March 2, 2004; 101(9): 2969 - 2974.
[Abstract] [Full Text] [PDF]


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J Exp BotHome page
S. Guyomarc'h, T. Vernoux, J. Traas, D.-X. Zhou, and M. Delarue
MGOUN3, an Arabidopsis gene with TetratricoPeptide-Repeat-related motifs, regulates meristem cellular organization
J. Exp. Bot., March 1, 2004; 55(397): 673 - 684.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
P. Muller-Moule, T. Golan, and K. K. Niyogi
Ascorbate-Deficient Mutants of Arabidopsis Grow in High Light Despite Chronic Photooxidative Stress
Plant Physiology, March 1, 2004; 134(3): 1163 - 1172.
[Abstract] [Full Text] [PDF]


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Plant CellHome page
R. B. Nair, K. L. Bastress, M. O. Ruegger, J. W. Denault, and C. Chapple
The Arabidopsis thaliana REDUCED EPIDERMAL FLUORESCENCE1 Gene Encodes an Aldehyde Dehydrogenase Involved in Ferulic Acid and Sinapic Acid Biosynthesis
PLANT CELL, February 1, 2004; 16(2): 544 - 554.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
C. D. Bosco, L. Lezhneva, A. Biehl, D. Leister, H. Strotmann, G. Wanner, and J. Meurer
Inactivation of the Chloroplast ATP Synthase {gamma} Subunit Results in High Non-photochemical Fluorescence Quenching and Altered Nuclear Gene Expression in Arabidopsis thaliana
J. Biol. Chem., January 9, 2004; 279(2): 1060 - 1069.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
T. L. Western, D. S. Young, G. H. Dean, W. L. Tan, A. L. Samuels, and G. W. Haughn
MUCILAGE-MODIFIED4 Encodes a Putative Pectin Biosynthetic Enzyme Developmentally Regulated by APETALA2, TRANSPARENT TESTA GLABRA1, and GLABRA2 in the Arabidopsis Seed Coat
Plant Physiology, January 1, 2004; 134(1): 296 - 306.
[Abstract] [Full Text] [PDF]




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