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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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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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 Plant CellHome page
L. B. Lai, J. A. Nadeau, J. Lucas, E.-K. Lee, T. Nakagawa, L. Zhao, M. Geisler, and F. D. Sack
The Arabidopsis R2R3 MYB Proteins FOUR LIPS and MYB88 Restrict Divisions Late in the Stomatal Cell Lineage
PLANT CELL, October 1, 2005; 17(10): 2754 - 2767.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
K. Ishizaki, T. R. Larson, N. Schauer, A. R. Fernie, I. A. Graham, and C. J. Leaver
The Critical Role of Arabidopsis Electron-Transfer Flavoprotein:Ubiquinone Oxidoreductase during Dark-Induced Starvation
PLANT CELL, September 1, 2005; 17(9): 2587 - 2600.
[Abstract] [Full Text] [PDF]

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 DevelopmentHome page
I. R. Henderson, F. Liu, S. Drea, G. G. Simpson, and C. Dean
An allelic series reveals essential roles for FY in plant development in addition to flowering-time control
Development, August 15, 2005; 132(16): 3597 - 3607.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
A. R. Thompson, J. H. Doelling, A. Suttangkakul, and R. D. Vierstra
Autophagic Nutrient Recycling in Arabidopsis Directed by the ATG8 and ATG12 Conjugation Pathways
Plant Physiology, August 1, 2005; 138(4): 2097 - 2110.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
N.-H. Cheng, J. K. Pittman, T. Shigaki, J. Lachmansingh, S. LeClere, B. Lahner, D. E. Salt, and K. D. Hirschi
Functional Association of Arabidopsis CAX1 and CAX3 Is Required for Normal Growth and Ion Homeostasis
Plant Physiology, August 1, 2005; 138(4): 2048 - 2060.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
A. Goyer, E. Collakova, R. D. de la Garza, E. P. Quinlivan, J. Williamson, J. F. Gregory III, Y. Shachar-Hill, and A. D. Hanson
5-Formyltetrahydrofolate Is an Inhibitory but Well Tolerated Metabolite in Arabidopsis Leaves
J. Biol. Chem., July 15, 2005; 280(28): 26137 - 26142.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
I. Pracharoenwattana, J. E. Cornah, and S. M. Smith
Arabidopsis Peroxisomal Citrate Synthase Is Required for Fatty Acid Respiration and Seed Germination
PLANT CELL, July 1, 2005; 17(7): 2037 - 2048.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
T. Nawy, J.-Y. Lee, J. Colinas, J. Y. Wang, S. C. Thongrod, J. E. Malamy, K. Birnbaum, and P. N. Benfey
Transcriptional Profile of the Arabidopsis Root Quiescent Center
PLANT CELL, July 1, 2005; 17(7): 1908 - 1925.
[Abstract] [Full Text] [PDF]

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 Plant Cell PhysiolHome page
T. Ito, R. Motohashi, T. Kuromori, Y. Noutoshi, M. Seki, A. Kamiya, S. Mizukado, T. Sakurai, and K. Shinozaki
A Resource of 5,814 Dissociation Transposon-tagged and Sequence-indexed Lines of Arabidopsis Transposed from Start Loci on Chromosome 5
Plant Cell Physiol., July 1, 2005; 46(7): 1149 - 1153.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
S. P. Briggs and T. Singer
Genetic Networks
Plant Physiology, June 1, 2005; 138(2): 542 - 544.
[Full Text] [PDF]

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 Plant CellHome page
F. Roudier, A. G. Fernandez, M. Fujita, R. Himmelspach, G. H.H. Borner, G. Schindelman, S. Song, T. I. Baskin, P. Dupree, G. O. Wasteneys, et al.
COBRA, an Arabidopsis Extracellular Glycosyl-Phosphatidyl Inositol-Anchored Protein, Specifically Controls Highly Anisotropic Expansion through Its Involvement in Cellulose Microfibril Orientation
PLANT CELL, June 1, 2005; 17(6): 1749 - 1763.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
A. Baldwin, A. Wardle, R. Patel, P. Dudley, S. K. Park, D. Twell, K. Inoue, and P. Jarvis
A Molecular-Genetic Study of the Arabidopsis Toc75 Gene Family
Plant Physiology, June 1, 2005; 138(2): 715 - 733.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
C. Vieira Dos Santos, S. Cuine, N. Rouhier, and P. Rey
The Arabidopsis Plastidic Methionine Sulfoxide Reductase B Proteins. Sequence and Activity Characteristics, Comparison of the Expression with Plastidic Methionine Sulfoxide Reductase A, and Induction by Photooxidative Stress
Plant Physiology, June 1, 2005; 138(2): 909 - 922.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
A. Feechan, E. Kwon, B.-W. Yun, Y. Wang, J. A. Pallas, and G. J. Loake
A central role for S-nitrosothiols in plant disease resistance
PNAS, May 31, 2005; 102(22): 8054 - 8059.
[Abstract] [Full Text] [PDF]


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