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First published online November 20, 2002; 10.1105/tpc.004630

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The Plant Cell, Vol. 14, 2985-2994, December 2002, Copyright © 2002,
American Society of Plant Biologists

GENOMICS ARTICLE

A High-Throughput Arabidopsis Reverse Genetics System

Allen Sessions1,a, Ellen Burkea, Gernot Prestinga, George Auxb, John McElverb, David Pattonb, Bob Dietrichb, Patrick Hoa, Johana Bacwadena, Cynthia Koa, Joseph D. Clarkea, David Cottona, David Bullisa, Jennifer Snella, Trini Miguela, Don Hutchisona, Bill Kimmerly2,a, Theresa Mitzelc, Fumiaki Katagiria, Jane Glazebrooka, Marc Lawb and Stephen A. Goffa

a Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, California 92121
b Syngenta Biotechnology Incorporated, 3054 Cornwallis Road, Research Triangle Park, North Carolina 27709
c Syngenta Seeds Incorporated, 7240 Holsclaw Road, Gilroy, California 95020

1 To whom correspondence should be addressed. E-mail allen.sessions{at}syngenta.com; fax 858-812-1337

A collection of Arabidopsis lines with T-DNA insertions in known sites was generated to increase the efficiency of functional genomics. A high-throughput modified thermal asymetric interlaced (TAIL)-PCR protocol was developed and used to amplify DNA fragments flanking the T-DNA left borders from ~100,000 transformed lines. A total of 85,108 TAIL-PCR products from 52,964 T-DNA lines were sequenced and compared with the Arabidopsis genome to determine the positions of T-DNAs in each line. Predicted T-DNA insertion sites, when mapped, showed a bias against predicted coding sequences. Predicted insertion mutations in genes of interest can be identified using Arabidopsis Gene Index name searches or by BLAST (Basic Local Alignment Search Tool) search. Insertions can be confirmed by simple PCR assays on individual lines. Predicted insertions were confirmed in 257 of 340 lines tested (76%). This resource has been named SAIL (Syngenta Arabidopsis Insertion Library) and is available to the scientific community at www.tmri.org.




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DNA demethylation in the Arabidopsis genome
PNAS, April 17, 2007; 104(16): 6752 - 6757.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
G. Leon, L. Holuigue, and X. Jordana
Mitochondrial Complex II Is Essential for Gametophyte Development in Arabidopsis
Plant Physiology, April 1, 2007; 143(4): 1534 - 1546.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
T. S. Hooker, P. Lam, H. Zheng, and L. Kunst
A Core Subunit of the RNA-Processing/Degrading Exosome Specifically Influences Cuticular Wax Biosynthesis in Arabidopsis
PLANT CELL, March 1, 2007; 19(3): 904 - 913.
[Abstract] [Full Text] [PDF]

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 Plant Cell PhysiolHome page
A. Iwama, T. Yamashino, Y. Tanaka, H. Sakakibara, T. Kakimoto, S. Sato, T. Kato, S. Tabata, A. Nagatani, and T. Mizuno
AHK5 Histidine Kinase Regulates Root Elongation Through an ETR1-Dependent Abscisic Acid and Ethylene Signaling Pathway in Arabidopsis thaliana
Plant Cell Physiol., February 1, 2007; 48(2): 375 - 380.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
M. W.B. Spencer, S. A. Casson, and K. Lindsey
Transcriptional Profiling of the Arabidopsis Embryo
Plant Physiology, February 1, 2007; 143(2): 924 - 940.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
Y. Li, M. G. Rosso, P. Viehoever, and B. Weisshaar
GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D874 - D878.
[Abstract] [Full Text] [PDF]

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 Plant Cell PhysiolHome page
J. H. Ahn, J. Kim, S. J. Yoo, S. Y. Yoo, H. Roh, J.-H. Choi, M. S. Choi, K. S. Chung, E. J. Han, S. M. Hong, et al.
Isolation of 151 Mutants that Have Developmental Defects from T-DNA Tagging
Plant Cell Physiol., January 1, 2007; 48(1): 169 - 178.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
L. J. Sweetlove, A. Lytovchenko, M. Morgan, A. Nunes-Nesi, N. L. Taylor, C. J. Baxter, I. Eickmeier, and A. R. Fernie
Mitochondrial uncoupling protein is required for efficient photosynthesis
PNAS, December 19, 2006; 103(51): 19587 - 19592.
[Abstract] [Full Text] [PDF]

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 Plant Cell PhysiolHome page
Y. Inoue, T. Suzuki, M. Hattori, K. Yoshimoto, Y. Ohsumi, and Y. Moriyasu
AtATG Genes, Homologs of Yeast Autophagy Genes, are Involved in Constitutive Autophagy in Arabidopsis Root Tip Cells
Plant Cell Physiol., December 1, 2006; 47(12): 1641 - 1652.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
J. Xu, J.-Y. Yang, Q.-W. Niu, and N.-H. Chua
Arabidopsis DCP2, DCP1, and VARICOSE Form a Decapping Complex Required for Postembryonic Development
PLANT CELL, December 1, 2006; 18(12): 3386 - 3398.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
V. Joshi, K. M. Laubengayer, N. Schauer, A. R. Fernie, and G. Jander
Two Arabidopsis Threonine Aldolases Are Nonredundant and Compete with Threonine Deaminase for a Common Substrate Pool
PLANT CELL, December 1, 2006; 18(12): 3564 - 3575.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
A. Galichet and W. Gruissem
Developmentally Controlled Farnesylation Modulates AtNAP1;1 Function in Cell Proliferation and Cell Expansion during Arabidopsis Leaf Development
Plant Physiology, December 1, 2006; 142(4): 1412 - 1426.
[Abstract] [Full Text] [PDF]

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 DevelopmentHome page
V. Exner, P. Taranto, N. Schonrock, W. Gruissem, and L. Hennig
Chromatin assembly factor CAF-1 is required for cellular differentiation during plant development
Development, November 1, 2006; 133(21): 4163 - 4172.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
S. Stegemann and R. Bock
Experimental Reconstruction of Functional Gene Transfer from the Tobacco Plastid Genome to the Nucleus
PLANT CELL, November 1, 2006; 18(11): 2869 - 2878.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
K.-i. Hibara, Md. R. Karim, S. Takada, K.-i. Taoka, M. Furutani, M. Aida, and M. Tasaka
Arabidopsis CUP-SHAPED COTYLEDON3 Regulates Postembryonic Shoot Meristem and Organ Boundary Formation
PLANT CELL, November 1, 2006; 18(11): 2946 - 2957.
[Abstract] [Full Text] [PDF]

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 DevelopmentHome page
S. Laubinger, V. Marchal, J. Gentilhomme, S. Wenkel, J. Adrian, S. Jang, C. Kulajta, H. Braun, G. Coupland, and U. Hoecker
Arabidopsis SPA proteins regulate photoperiodic flowering and interact with the floral inducer CONSTANS to regulate its stability
Development, August 15, 2006; 133(16): 3213 - 3222.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
J. Stockel, S. Bennewitz, P. Hein, and R. Oelmuller
The Evolutionarily Conserved Tetratrico Peptide Repeat Protein Pale Yellow Green7 Is Required for Photosystem I Accumulation in Arabidopsis and Copurifies with the Complex
Plant Physiology, July 1, 2006; 141(3): 870 - 878.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
E. R. Morris, D. Chevalier, and J. C. Walker
DAWDLE, a Forkhead-Associated Domain Gene, Regulates Multiple Aspects of Plant Development
Plant Physiology, July 1, 2006; 141(3): 932 - 941.
[Abstract] [Full Text] [PDF]

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 Genes Dev.Home page
N. Schonrock, R. Bouveret, O. Leroy, L. Borghi, C. Kohler, W. Gruissem, and L. Hennig
Polycomb-group proteins repressthe floral activator AGL19 in the FLC-independent vernalization pathway.
Genes & Dev., June 15, 2006; 20(12): 1667 - 1678.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
P. L. Conklin, S. Gatzek, G. L. Wheeler, J. Dowdle, M. J. Raymond, S. Rolinski, M. Isupov, J. A. Littlechild, and N. Smirnoff
Arabidopsis thaliana VTC4 Encodes L-Galactose-1-P Phosphatase, a Plant Ascorbic Acid Biosynthetic Enzyme
J. Biol. Chem., June 9, 2006; 281(23): 15662 - 15670.
[Abstract] [Full Text] [PDF]

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 Plant Cell PhysiolHome page
N. Nakagawa and N. Sakurai
A Mutation in At-nMat1a, Which Encodes a Nuclear Gene Having High Similarity to Group II Intron Maturase, Causes Impaired Splicing of Mitochondrial NAD4 Transcript and Altered Carbon Metabolism in Arabidopsis thaliana
Plant Cell Physiol., June 1, 2006; 47(6): 772 - 783.
[Abstract] [Full Text] [PDF]

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 DevelopmentHome page
R. Bouveret, N. Schonrock, W. Gruissem, and L. Hennig
Regulation of flowering time by Arabidopsis MSI1
Development, May 1, 2006; 133(9): 1693 - 1702.
[Abstract] [Full Text] [PDF]

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 Plant Cell PhysiolHome page
K. Nakajima, T. Kawamura, and T. Hashimoto
Role of the SPIRAL1 Gene Family in Anisotropic Growth of Arabidopsis thaliana
Plant Cell Physiol., April 1, 2006; 47(4): 513 - 522.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
P. Pesaresi, S. Masiero, H. Eubel, H.-P. Braun, S. Bhushan, E. Glaser, F. Salamini, and D. Leister
Nuclear Photosynthetic Gene Expression Is Synergistically Modulated by Rates of Protein Synthesis in Chloroplasts and Mitochondria
PLANT CELL, April 1, 2006; 18(4): 970 - 991.
[Abstract] [Full Text] [PDF]

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 J Exp BotHome page
I. Scott, A. K. Tobin, and D. C. Logan
BIGYIN, an orthologue of human and yeast FIS1 genes functions in the control of mitochondrial size and number in Arabidopsis thaliana
J. Exp. Bot., March 1, 2006; 57(6): 1275 - 1280.
[Abstract] [Full Text] [PDF]

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 Mol. Biol. CellHome page
A. J. Wijeratne, C. Chen, W. Zhang, L. Timofejeva, and H. Ma
The Arabidopsis thaliana PARTING DANCERS Gene Encoding a Novel Protein Is Required for Normal Meiotic Homologous Recombination
Mol. Biol. Cell, March 1, 2006; 17(3): 1331 - 1343.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
T. J. Emborg, J. M. Walker, B. Noh, and R. D. Vierstra
Multiple Heme Oxygenase Family Members Contribute to the Biosynthesis of the Phytochrome Chromophore in Arabidopsis
Plant Physiology, March 1, 2006; 140(3): 856 - 868.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
Q. K.-G. Tan and V. F. Irish
The Arabidopsis Zinc Finger-Homeodomain Genes Encode Proteins with Unique Biochemical Properties That Are Coordinately Expressed during Floral Development
Plant Physiology, March 1, 2006; 140(3): 1095 - 1108.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
J. C. Coates, L. Laplaze, and J. Haseloff
Armadillo-related proteins promote lateral root development in Arabidopsis
PNAS, January 31, 2006; 103(5): 1621 - 1626.
[Abstract] [Full Text] [PDF]

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 J Exp BotHome page
R. S. Quilliam, P. J. Swarbrick, J. D. Scholes, and S. A. Rolfe
Imaging photosynthesis in wounded leaves of Arabidopsis thaliana
J. Exp. Bot., January 1, 2006; 57(1): 55 - 69.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
M. Riefler, O. Novak, M. Strnad, and T. Schmulling
Arabidopsis Cytokinin Receptor Mutants Reveal Functions in Shoot Growth, Leaf Senescence, Seed Size, Germination, Root Development, and Cytokinin Metabolism
PLANT CELL, January 1, 2006; 18(1): 40 - 54.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
A. J. Manfre, L. M. Lanni, and W. R. Marcotte Jr.
The Arabidopsis Group 1 LATE EMBRYOGENESIS ABUNDANT Protein ATEM6 Is Required for Normal Seed Development
Plant Physiology, January 1, 2006; 140(1): 140 - 149.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
C. Albrecht, E. Russinova, V. Hecht, E. Baaijens, and S. de Vries
The Arabidopsis thaliana SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES1 and 2 Control Male Sporogenesis
PLANT CELL, December 1, 2005; 17(12): 3337 - 3349.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
P. J. Overvoorde, Y. Okushima, J. M. Alonso, A. Chan, C. Chang, J. R. Ecker, B. Hughes, A. Liu, C. Onodera, H. Quach, et al.
Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID Gene Family Members in Arabidopsis thaliana
PLANT CELL, December 1, 2005; 17(12): 3282 - 3300.
[Abstract] [Full Text] [PDF]


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