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Plant Physiol, December 2000, Vol. 124, pp. 1465-1467
The Arabidopsis Knockout Facility at the University of
Wisconsin-Madison1
Michael R.
Sussman,*
Richard M.
Amasino,
Jeffery C.
Young,
Patrick J.
Krysan, and
Sandra
Austin-Phillips
Biotechnology Center (M.R.S., P.J.K., S.A.-P.) and Department of
Biochemistry (R.M.A.), University of Wisconsin, Madison, Wisconsin
53706; and Biology Department, Western Washington University,
Bellingham, Washington 98225 (J.C.Y.)
 |
INTRODUCTION |
As of this writing the
Arabidopsis genome is 97% sequenced with only small portions of the
highly repetitive regions within centromeres and telomeres remaining.
The identification of approximately 25,000 plant genes will give plant
biologists an opportunity to identify and understand the function
of the proteins they encode. One exciting tool that will aid in this
endeavor is the use of insertional mutagenesis to create "gene
knockouts." The availability of a mutant line in which the action of
a known, specific gene has been disrupted gives the plant biologist a
powerful tool in understanding the action of that gene. The basis of
this approach is to create a large population of plants containing
randomly inserted pieces of foreign DNA. If the sequence of a gene is
known, it is possible to devise a PCR-based strategy to identify a
plant where that specific gene has been disrupted by the
insertion of foreign DNA. To fully utilize this technology it is
necessary to saturate the genome with insertion mutations and to
develop efficient PCR-based screening methods to comb through knockout plant populations and identify specific mutant plants. The smaller the
gene, the more difficult a target it represents, and thus hundreds of
thousands of lines are needed to provide a high probability that a
particular gene is present as a knockout in the population.
As a beginning, a method has been developed for rapidly searching a
large collection of T-DNA transformed Arabidopsis lines for the
presence of T-DNA inserts within specific genes (Krysan et al., 1996 ,
1999). To use this technology, a collection of 60,480 Arabidopsis
(accession Wassilewskija [WS]) lines were generated that were
transformed with the T-DNA vector pD991. Preliminary data from
screening this collection indicated that this collection could indeed
be efficiently screened for mutant lines. To share this resource with
all members of the Arabidopsis research community, a "Knockout
Facility" was established at the University of Wisconsin (Madison) in
1999 as part of the Arabidopsis Functional Genomics Consortium. A
detailed description of this initial population and the operation of
the facility have been given in a recent publication (Krysan et al.,
1999) and is described more fully at the website
http://www. biotech.wisc.edu/Arabidopsis.
In this brief note we will give an overview of the first year's
operation and describe our future plans. We strongly advice that users
read the web site fully before using the facility and contact us with
any questions that they may have.
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CURRENT FACILITY OPERATION |
The facility is housed in the Plant Biotechnology Laboratory at
the University of Wisconsin Biotechnology Center located at 425 Henry
Mall, University of Wisconsin, Madison, WI 53706. The fee-for-service
operation relies heavily on the administrative and information services
of the Biotechnology Center. Users interact with the facility through
the website. The site has a full description of the PCR screening
including primer design and subsequent analysis of the PCR products.
Primer design is a critical element of the screening process and users
are asked to test their primers before sending them to the facility.
Each user has their own personal web page on the site allowing them to
track their screens. Our current resources are organized as
follows:
Seed: 6,720 pools of 9
DNA Preps: 270 pools of 225
DNA Super Pools: 30 super pools (9 pools of 225 per super pool;
2,025 lines per super pool)
Researchers basically send us PCR primers for a gene for which
they want a "knock-out." We perform PCR reactions using our DNA
pools and the researcher's PCR primers. We then send the PCR reactions
to the users to analyze. Our PCR strategy is composed of two rounds of
PCR. The first round of PCR searches the entire population for T-DNA
inserts in the gene. This set of reactions uses the researcher's gene
primers and one T-DNA border primer and the 30 DNA super pools. If a
hit is found in the first round of PCR then a second round is performed
which narrows down the hit to one particular pool of 225. Last of
all, the researchers request seed from the 25 pools of 9, which correspond to that pool of 225. One of these tubes of seed will
contain the knockout. The researchers will then search within this
population for the plant(s) in which their gene is disrupted. The
organization and screening strategy is summarized in Figure 1.
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RESULTS TO DATE |
The laboratories of over 360 Principal Investigators are currently
using the Knockout Facility; 60% of these are from North America, 25%
are from Europe, and the remainder are from other parts of the world.
As of August 2000, over 1,300 first-round and 900 second-round screens
have been performed. About 60% of users have found at least one hit in
their first round screens. Some users choose to follow more than one
hit. It is still too soon to accurately assess the number of screens
that ultimately result in mutant plants with a useful phenotype.
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FUTURE PLANS |
Additional Populations
Although the current population has successfully identified
knockouts for many users, there is obviously a need to incorporate additional populations into the screening process. We have generated a
further 72,960 BASTA (glufosinate)-resistant lines transformed with an activation-Tag vector, pSK1015 (Weigel et al., 2000). Full
details of the vector used and the screening process are given on the
web site. This population will be available at the beginning of 2001. Seed for these lines is organized as pools of 10 in a 96-well format
and the DNA is organized in a three-dimensional grid. This allows us to
localize a knockout to a single pool of 10 plants after only two PCR
rounds. This is obviously much more efficient for the user who
currently has to find their knockout from 25 pools of nine plants. The
primer design for this population is identical. Additional populations
developed at the University of Wisconsin, Yale University, and other
locations will be incorporated into the facility as they become
available. It should be noted that for this large-scale effort aimed at
saturating the genome, useful populations require a minimum of many
tens of thousands of individual lines organized in pools of less than
10 lines each.
User Feedback
Screens are currently confidential and we do not maintain a
database of genes or sequences for which a knockout has been obtained. This obviously leads to duplication of effort, but not all researchers are comfortable with their research efforts being public before the
work is published. We intend to establish a searchable database on our
website where users can voluntarily list their primer sequences and the
outcome of their screens. We will also develop a survey for user
feedback that will give basic information on the actual insertion events.
Long-Term Goals
PCR screening has proven to be an effective method of identifying
plant knockouts. An even more efficient alternative would be to catalog
all of the locations of the T-DNA inserts within the population using a
sequence tag. This database of T-DNA flanking sequences could be
searched for the presence of flanking sequences homologous to any gene
of interest, thus identifying a knockout plant.
Pilot studies are currently in progress to develop a high throughput
procedure, e.g. using thermal asymmetric interlaced PCR to
accomplish the sequencing. Efforts are now under way to analyze thousands of flanking sequences from individual lines. It will be
necessary to have hundreds of thousands of such sequences to be a fully
comprehensive database. Since this may take several years to create, we
intend to keep the PCR-based screening facility as a parallel effort
until the database of sequences is sufficiently large to ensure that
researchers are certain to obtain knockout plants in their gene of
interest. Researchers have also found it extremely useful to obtain
more than one allele, i.e. knockouts created by insertions in various
locations within the gene. Such multiple alleles are useful to be sure
that resultant phenotypes are in fact due to the insertion rather than
mutations located nearby, but not within the gene of interest.
Future populations will contain transposons located within the
T-DNA to allow a line to be developed in which neighboring genes are
disrupted. The current method of creating "double knockouts" involves first isolating individual knockout lines and then crossing them into the same plant. For genes that are located within a few
thousand bases of each other this method would require the screening of
an unreasonable number of recombinants. The alternative method of using
the first insertion line as a "launching pad" for transposon
elements to land nearby represents a more reasonable and viable approach.
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ACKNOWLEDGMENTS |
The authors thank Sean Monson, Laura Katers, Sarah Benn,
Kiersten Iovinella, and Erin Olsen for technical assistance in the Knockout Facility.
| |
FOOTNOTES |
Received September 1, 2000; accepted September 22, 2000.
1
This work was supported by the National Science
Foundation (grant no. DBI 9872638).
*
Corresponding author; e-mail msussman{at}facstaff.wisc.edu; fax
608-262-6748
| |
LITERATURE CITED |
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Krysan PJ, Young JC, Sussman MR
(1999)
T-DNA as an insertional mutagen in Arabidopsis.
Plant Cell
11: 2283-2290
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Krysan PJ, Young JC, Tax F, Sussman MR
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Identification of transferred DNA insertions within Arabidopsis genes involved in signal transduction and ion transport.
Proc Natl Acad Sci USA
93: 8145-8150
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Weigel D, Ahn JH, Blazquez MA, Borevitz JO, Christensen SK, Fankhauser C, Ferrandiz C, Kardailsky I, Malancharuvil EJ, Neff MM, Nguyen JT, Sato S, Wang ZY, Xia Y, Dixon RA, Harrison MJ, Lamb CJ, Yanofsky MF, Chory J
(2000)
Activation tagging in Arabidopsis.
Plant Physiol
122: 1003-1013
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© 2000 American Society of Plant Physiologists
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June 6, 2003;
278(24):
21370 - 21377.
[Abstract]
[Full Text]
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J. O. Borevitz and M. Nordborg
The Impact of Genomics on the Study of Natural Variation in Arabidopsis
Plant Physiology,
June 1, 2003;
132(2):
718 - 725.
[Full Text]
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G. Bonaventure, J. J. Salas, M. R. Pollard, and J. B. Ohlrogge
Disruption of the FATB Gene in Arabidopsis Demonstrates an Essential Role of Saturated Fatty Acids in Plant Growth
PLANT CELL,
April 1, 2003;
15(4):
1020 - 1033.
[Abstract]
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I. Steinebrunner, J. Wu, Y. Sun, A. Corbett, and S. J. Roux
Disruption of Apyrases Inhibits Pollen Germination in Arabidopsis
Plant Physiology,
April 1, 2003;
131(4):
1638 - 1647.
[Abstract]
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L. Lopez-Molina, S. Mongrand, N. Kinoshita, and N.-H. Chua
AFP is a novel negative regulator of ABA signaling that promotes ABI5 protein degradation
Genes & Dev.,
February 1, 2003;
17(3):
410 - 418.
[Abstract]
[Full Text]
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A. Sessions, E. Burke, G. Presting, G. Aux, J. McElver, D. Patton, B. Dietrich, P. Ho, J. Bacwaden, C. Ko, et al.
A High-Throughput Arabidopsis Reverse Genetics System
PLANT CELL,
December 1, 2002;
14(12):
2985 - 2994.
[Abstract]
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C. J. Schultz, M. P. Rumsewicz, K. L. Johnson, B. J. Jones, Y. M. Gaspar, and A. Bacic
Using Genomic Resources to Guide Research Directions. The Arabinogalactan Protein Gene Family as a Test Case
Plant Physiology,
August 1, 2002;
129(4):
1448 - 1463.
[Abstract]
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F. M. Ausubel
Summaries of National Science Foundation-Sponsored Arabidopsis 2010 Projects and National Science Foundation-Sponsored Plant Genome Projects That Are Generating Arabidopsis Resources for the Community
Plant Physiology,
June 1, 2002;
129(2):
394 - 437.
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G. Jander, S. R. Norris, S. D. Rounsley, D. F. Bush, I. M. Levin, and R. L. Last
Arabidopsis Map-Based Cloning in the Post-Genome Era
Plant Physiology,
June 1, 2002;
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[Abstract]
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M. Holm, L.-G. Ma, L.-J. Qu, and X.-W. Deng
Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis
Genes & Dev.,
May 15, 2002;
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1247 - 1259.
[Abstract]
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F. Rolland, B. Moore, and J. Sheen
Sugar Sensing and Signaling in Plants
PLANT CELL,
May 1, 2002;
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B. Yu, C. Xu, and C. Benning
Arabidopsis disrupted in SQD2 encoding sulfolipid synthase is impaired in phosphate-limited growth
PNAS,
April 16, 2002;
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5732 - 5737.
[Abstract]
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A. Weber and U.-I. Flugge
Interaction of cytosolic and plastidic nitrogen metabolism in plants
J. Exp. Bot.,
April 15, 2002;
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[Abstract]
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J. Sheen
Signal Transduction in Maize and Arabidopsis Mesophyll Protoplasts
Plant Physiology,
December 1, 2001;
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[Abstract]
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Y.-L. Chang, Q. Tao, C. Scheuring, K. Ding, K. Meksem, and H.-B. Zhang
An Integrated Map of Arabidopsis thaliana for Functional Analysis of Its Genome Sequence
Genetics,
November 1, 2001;
159(3):
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[Abstract]
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J. Li, K. A. Lease, F. E. Tax, and J. C. Walker
BRS1, a serine carboxypeptidase, regulates BRI1 signaling in Arabidopsis thaliana
PNAS,
April 18, 2001;
(2001)
91065998.
[Abstract]
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F. M. Ausubel
Arabidopsis Genome. A Milestone in Plant Biology
Plant Physiology,
December 1, 2000;
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[Full Text]
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J. Li, K. A. Lease, F. E. Tax, and J. C. Walker
BRS1, a serine carboxypeptidase, regulates BRI1 signaling in Arabidopsis thaliana
PNAS,
May 8, 2001;
98(10):
5916 - 5921.
[Abstract]
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[PDF]
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TOP
INTRODUCTION
CURRENT FACILITY OPERATION