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First published online February 24, 2002; 10.1104/pp.010681

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Plant Physiol, March 2002, Vol. 128, pp. 896-910

Comparison of RNA Expression Profiles Based on Maize Expressed Sequence Tag Frequency Analysis and Micro-Array Hybridization1

John Fernandes, Volker Brendel, Xiaowu Gai, Shailesh Lal, Vicki L. Chandler, Rangasamy P. Elumalai, David W. Galbraith, Elizabeth A. Pierson, and Virginia Walbot*

Department of Biological Sciences, Stanford University, Stanford, California 94305-5020 (J.F., V.W.); Departments of Zoology and Genetics (V.B., X.G., S.L.) and Statistics (V.B.), Iowa State University, Ames, Iowa 50011-3260; and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721-0001 (V.L.C., R.P.E., D.W.G., E.A.P.)

Assembly of 73,000 expressed sequence tags (ESTs) representing multiple organs and developmental stages of maize (Zea mays) identified approximately 22,000 tentative unique genes (TUGs) at the criterion of 95% identity. Based on sequence similarity, overlap between any two of nine libraries with more than 3,000 ESTs ranged from 4% to 20% of the constituent TUGs. The most abundant ESTs were recovered from only one or a minority of the libraries, and only 26 EST contigs had members from all nine EST sets (presumably representing ubiquitously expressed genes). For several examples, ESTs for different members of gene families were detected in distinct organs. To study this further, two types of micro-array slides were fabricated, one containing 5,534 ESTs from 10- to 14-d-old endosperm, and the other 4,844 ESTs from immature ear, estimated to represent about 2,800 and 2,500 unique genes, respectively. Each array type was hybridized with fluorescent cDNA targets prepared from endosperm and immature ear poly(A+) RNA. Although the 10- to 14-d-old postpollination endosperm TUGs showed only 12% overlap with immature ear TUGs, endosperm target hybridized with 94% of the ear TUGs, and ear target hybridized with 57% of the endosperm TUGs. Incomplete EST sampling of low-abundance transcripts contributes to an underestimate of shared gene expression profiles. Reassembly of ESTs at the criterion of 90% identity suggests how cross hybridization among gene family members can overestimate the overlap in genes expressed in micro-array hybridization experiments.

1 This work was supported by the National Science Foundation Plant Genome Research Program as part of the Maize Gene Discovery, DNA Sequencing, and Phenotypic Analysis project (grant no. DBI-9872657).

* Corresponding author; e-mail walbot{at}stanford.edu; fax 650-725-8221.

© 2002 American Society of Plant Physiologists


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