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Plant Physiology 135:1206-1220 (2004)
© 2004 American Society of Plant Biologists

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GENOME ANALYSIS

Identification of Genes Required for Embryo Development in Arabidopsis1,[w]

Iris Tzafrir, Rosanna Pena-Muralla, Allan Dickerman, Michael Berg, Rebecca Rogers, Steven Hutchens, T. Colleen Sweeney, John McElver2, George Aux, David Patton and David Meinke*

Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078 (I.T., R.P.M., M.B., R.R., S.H., T.C.S., D.M.); Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 (A.D.); and Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (J.M., G.A., D.P.)

A long-term goal of Arabidopsis research is to define the minimal gene set needed to produce a viable plant with a normal phenotype under diverse conditions. This will require both forward and reverse genetics along with novel strategies to characterize multigene families and redundant biochemical pathways. Here we describe an initial dataset of 250 EMB genes required for normal embryo development in Arabidopsis. This represents the first large-scale dataset of essential genes in a flowering plant. When compared with 550 genes with other knockout phenotypes, EMB genes are enriched for basal cellular functions, deficient in transcription factors and signaling components, have fewer paralogs, and are more likely to have counterparts among essential genes of yeast (Saccharomyces cerevisiae) and worm (Caenorhabditis elegans). EMB genes also represent a valuable source of plant-specific proteins with unknown functions required for growth and development. Analyzing such unknowns is a central objective of genomics efforts worldwide. We focus here on 34 confirmed EMB genes with unknown functions, demonstrate that expression of these genes is not embryo-specific, validate a strategy for identifying interacting proteins through complementation with epitope-tagged proteins, and discuss the value of EMB genes in identifying novel proteins associated with important plant processes. Based on sequence comparison with essential genes in other model eukaryotes, we identify 244 candidate EMB genes without paralogs that represent promising targets for reverse genetics. These candidates should facilitate the recovery of additional genes required for seed development.

1 This work was supported by the NSF Developmental Mechanisms and Arabidopsis 2010 Programs and the S.R. Noble Foundation (Ardmore, OK).

2 Present address: BASF Plant Science, Research Triangle Park, NC 27709.

[w] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.104.045179.

* Corresponding author; e-mail meinke{at}okstate.edu; fax 405–744–7074.

Received April 23, 2004; returned for revision May 19, 2004; accepted May 21, 2004.




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