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First published online November 18, 2005; 10.1104/pp.105.067314 Plant Physiology 139:1853-1869 (2005) © 2005 American Society of Plant Biologists Analysis of the Female Gametophyte Transcriptome of Arabidopsis by Comparative Expression Profiling1,[W]Section of Plant Biology (H.-J.Y., P.H., V.S.) and Department of Plant Sciences (V.S.), University of California, Davis, California 95616; and National Horticultural Research Institute, Rural Development Administration, Suwon 440–706, Korea (H.-J.Y.)
The extensive data on the transcription of the plant genome are derived primarily from the sporophytic generation. There currently is little information on genes that are expressed during female gametophyte development in angiosperms, and it is not known whether the female gametophyte transcriptome contains a major set of genes that are not expressed in the sporophyte or whether it is primarily a subset of the sporophytic transcriptome. Because the embryo sac is embedded within the maternal ovule tissue, we have utilized the Arabidopsis (Arabidopsis thaliana) mutant sporocyteless that produces ovules without embryo sacs, together with the ATH1 Arabidopsis whole-genome oligonucleotide array, to identify genes that are preferentially or specifically expressed in female gametophyte development. From analysis of the datasets, 225 genes are identified as female gametophyte genes, likely a lower limit as stringent criteria were used for the analysis, eliminating many low expressed genes. Nearly 45% of the identified genes were not previously detected by sporophytic expression profiling, suggesting that the embryo sac transcriptome may contain a significant fraction of transcripts restricted to the gametophyte. Validation of six candidate genes was performed using promoter::
1 This work was supported by the National Science Foundation (NSF2010 program grant no. 0313501 to V.S.). H.-J.Y. received fellowship support from Korea Science and Engineering Foundation (KOSEF). The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Venkatesan Sundaresan (sundar{at}ucdavis.edu). [W] The online version of this article contains Web-only data. Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.105.067314. * Corresponding author; e-mail sundar{at}ucdavis.edu; fax 530–752–5410. Received June 20, 2005; returned for revision September 30, 2005; accepted October 3, 2005. Related articles in Plant Physiol.:
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-glucuronidase fusions, and all of these showed embryo sac-specific expression in the ovule. The unfiltered expression data from this study can be used to evaluate the possibility of female gametophytic expression for any gene in the ATH1 array, and contribute to identification of the functions of the component of the Arabidopsis genome not represented in studies of sporophytic expression and function. 
