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First published online June 17, 2005; 10.1104/pp.104.057638 Plant Physiology 138:1700-1710 (2005) © 2005 American Society of Plant Biologists The Maize Root Transcriptome by Serial Analysis of Gene Expression1,[w]Department of Plant Biology (V.P., H.J.B.) and Department of Crop Sciences (H.J.B.), University of Illinois, Urbana, Illinois 61801; and Division of Plant Sciences, Plant Sciences Unit (L.G.H., W.G.S., H.T.N., R.E.S.), and Department of Computer Science (G.K.S.), University of Missouri, Columbia, Missouri 65211–7145
Serial Analysis of Gene Expression was used to define number and relative abundance of transcripts in the root tip of well-watered maize seedlings (Zea mays cv FR697). In total, 161,320 tags represented a minimum of 14,850 genes, based on at least two tags detected per transcript. The root transcriptome has been sampled to an estimated copy number of approximately five transcripts per cell. An extrapolation from the data and testing of single-tag identifiers by reverse transcription-PCR indicated that the maize root transcriptome should amount to at least 22,000 expressed genes. Frequency ranged from low copy number (2–5, 68.8%) to highly abundant transcripts (100
1 This work was supported by the National Science Foundation (grant nos. DBI–0223905 and DBI–0211842) and by University of Illinois Urbana-Champaign and University of Missouri institutional grants. [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.104.057638. * Corresponding author; e-mail bohnerth{at}life.uiuc.edu; fax 217–333–5574. Received January 26, 2005; returned for revision March 15, 2005; accepted March 21, 2005. Related articles in Plant Physiol.:
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1,200; 1%). Quantitative reverse transcription-PCR for selected transcripts indicated high correlation with tag frequency. Computational analysis compared this set with known maize transcripts and other root transcriptome models. Among the 14,850 tags, 7,010 (47%) were found for which no maize cDNA or gene model existed. Comparing the maize root transcriptome with that in other plants indicated that highly expressed transcripts differed substantially; less than 5% of the most abundant transcripts were shared between maize and Arabidopsis (Arabidopsis thaliana). Transcript categories highlight functions of the maize root tip. Significant variation in abundance characterizes transcripts derived from isoforms of individual enzymes in biochemical pathways. 
