DOI: 10.1073/pnas.1831119100. Maize-targeted mutagenesis: A knockout resource for maize

Maize-targeted mutagenesis: A knockout resource for maize

10.1073/pnas.1831119100

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

We describe an efficient system for site-selected transposon mutagenesis in maize. A total of 43,776 F 1 plants were generated by using Robertson's Mutator ( Mu ) pollen parents and self-pollinated to establish a library of transposon-mutagenized seed. The frequency of new seed mutants was between 10 –4 and 10 –5 per F 1 plant. As a service to the maize community, maize-targeted mutagenesis selects insertions in genes of interest from this library by using the PCR. Pedigree, knockout, sequence, phenotype, and other information is stored in a powerful interactive database (maize-targeted mutagenesis database) that enables analysis of the entire population and the handling of knockout requests. By inhibiting Mu activity in most F 1 plants, we sought to reduce somatic insertions that may cause false positives selected from pooled tissue. By monitoring the remaining Mu activity in the F 2 , however, we demonstrate that seed phenotypes depend on it, and false positives occur in lines that appear to lack it. We conclude that more than half of all mutations arising in this population are suppressed on losing Mu activity. These results have implications for epigenetic models of inbreeding and for functional genomics.

Bibliography

May, B. P., Liu, H., Vollbrecht, E., Senior, L., Rabinowicz, P. D., Roh, D., Pan, X., Stein, L., Freeling, M., Alexander, D., & Martienssen, R. (2003). Maize-targeted mutagenesis: A knockout resource for maize. Proceedings of the National Academy of Sciences, 100(20), 11541â11546.

Authors 11

Bruce P. May (first)
Hong Liu (additional)
Erik Vollbrecht (additional)
Lynn Senior (additional)
Pablo D. Rabinowicz (additional)
Donna Roh (additional)
Xiaokang Pan (additional)
Lincoln Stein (additional)
Mike Freeling (additional)
Danny Alexander (additional)
Rob Martienssen (additional)

References 40 Referenced 96

10.1073/pnas.95.5.2021
Lee, K. Y., Lund, P., Lowe, K. & Dunsmuir, P. (1990) Plant Cell 2, 415–425.2152167 / Plant Cell (1990)
10.1046/j.1365-313X.1995.7020359.x
10.1073/pnas.87.5.1686
10.1073/pnas.90.16.7431
10.1104/pp.124.4.1465
10.1105/tpc.11.10.1853
10.1073/pnas.92.18.8149
Das, L. & Martienssen, R. (1995) Plant Cell 7, 287–294.7734963 / Plant Cell (1995)
Bensen, R. J., Johal, G. S., Crane, V. C., Tossberg, J. T., Schnable, P. S., Meeley, R. B. & Briggs, S. P. (1995) Plant Cell 7, 75–84.7696880 / Plant Cell (1995)
10.1126/science.274.5292.1537
10.1016/S0065-2660(08)60319-3
Bennetzen, J. L. (1996) Curr. Top. Microbiol. Immunol. 204, 195–229.8556867 / Curr. Top. Microbiol. Immunol. (1996)
10.1093/genetics/112.1.107
10.1016/0027-5107(78)90004-0
10.1046/j.1365-313x.2000.00830.x
10.1093/genetics/139.4.1777
10.1093/genetics/129.1.261
Chen J. & Dellaporta S. L. (1994) in The Maize Handbook eds. Freeling M. & Walbot V. (Springer New York) pp. 526–527. (10.1007/978-1-4612-2694-9_85)
Wall L. Orwant J. & Christiansen T. (2000) Programming Perl (O'Reilly and Associates Sebastopol CA).
10.1101/gr.8.12.1308
Stein L. (1999) The Official Guide to CGI.pm (Wiley New York).
10.1093/genetics/130.4.889
10.1093/genetics/136.3.1157
10.1101/gad.6.4.609
10.1016/0092-8674(91)90436-3
Martienssen R. (1996) in Epigenetic Mechanisms of Gene Regulation eds. Russo V. E. A. Martienssen R. & Riggs A. D. (Cold Spring Harbor Lab. Press Plainview NY) pp. 593–608.
10.1038/15479
10.1093/genetics/160.2.697
McClintock, B. (1954) Carnegie Inst. Washington Year Book 53, 254–260. / Carnegie Inst. Washington Year Book (1954)
McClintock, B. (1958) Carnegie Inst. Washington Year Book 57, 415–429. / Carnegie Inst. Washington Year Book (1958)
10.1093/genetics/157.1.349
10.1073/pnas.88.8.3502
10.1093/genetics/154.1.437
Vollbrecht, E., Reiser, L. & Hake, S. (2000) Development (Cambridge, U.K.) 127, 3161–3172. / Development (Cambridge, U.K.) (2000)
10.1093/genetics/163.2.685
10.1080/713610849
10.1105/TPC.010002
10.1016/S0168-9525(98)01518-2
10.1093/genetics/143.1.489

Dates

Type	When
Created	21 years, 10 months ago (Oct. 1, 2003, 3:44 p.m.)
Deposited	3 years, 4 months ago (April 13, 2022, 4:59 a.m.)
Indexed	1 month, 4 weeks ago (July 1, 2025, 5:10 p.m.)
Issued	21 years, 11 months ago (Sept. 3, 2003)
Published	21 years, 11 months ago (Sept. 3, 2003)
Published Online	21 years, 11 months ago (Sept. 3, 2003)
Published Print	21 years, 11 months ago (Sept. 30, 2003)

Funders 0

None

BibTeX

@article{May_2003, title={Maize-targeted mutagenesis: A knockout resource for maize}, volume={100}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.1831119100}, DOI={10.1073/pnas.1831119100}, number={20}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={May, Bruce P. and Liu, Hong and Vollbrecht, Erik and Senior, Lynn and Rabinowicz, Pablo D. and Roh, Donna and Pan, Xiaokang and Stein, Lincoln and Freeling, Mike and Alexander, Danny and Martienssen, Rob}, year={2003}, month=sep, pages={11541–11546} }

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