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Plant Physiology 134:960-968 (2004)
© 2004 American Society of Plant Biologists

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BIOINFORMATICS

A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age1

Timothy J. Close, Steve I. Wanamaker, Rico A. Caldo, Stacy M. Turner, Daniel A. Ashlock, Julie A. Dickerson, Rod A. Wing, Gary J. Muehlbauer, Andris Kleinhofs and Roger P. Wise*

Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (T.J.C., S.I.W.); Departments of Plant Pathology and Center for Plant Responses to Environmental Stresses (R.A.C., S.M.T., R.P.W.), Computer and Electrical Engineering (J.A.D.), Mathematics (D.A.A.), Interdepartmental Bioinformatics and Computational Biology (S.M.T., D.A.A., J.A.D., R.P.W.), and Corn Insects and Crop Genetics Research, United States Department of Agriculture (USDA)-Agricultural Research Service (R.P.W.), Iowa State University, Ames, Iowa 50011; Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721 (R.A.W.); Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (G.J.M.); and Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164 (A.K.)

In recent years, access to complete genomic sequences, coupled with rapidly accumulating data related to RNA and protein expression patterns, has made it possible to determine comprehensively how genes contribute to complex phenotypes. However, for major crop plants, publicly available, standard platforms for parallel expression analysis have been limited. We report the conception and design of the new publicly available, 22K Barley1 GeneChip probe array, a model for plants without a fully sequenced genome. Array content was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley (Hordeum vulgare) gene sequences from the National Center for Biotechnology Information nonredundant database. Conserved sequences expressed in seedlings of wheat (Triticum aestivum), oat (Avena strigosa), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays) were identified that will be valuable in the design of arrays across grasses. To enhance the usability of the data, BarleyBase, a MIAME-compliant, MySQL relational database, serves as a public repository for raw and normalized expression data from the Barley1 GeneChip probe array. Interconnecting links with PlantGDB and Gramene allow BarleyBase users to perform gene predictions using the 21,439 non-redundant Barley1 exemplar sequences or cross-species comparison at the genome level, respectively. We expect that this first generation array will accelerate hypothesis generation and gene discovery in disease defense pathways, responses to abiotic stresses, development, and evolutionary diversity in monocot plants.

http://www.plantphysiol.org/cgi/doi/10.1104/pp.103.034462.

1 This work was supported by the USDA (Initiative for Future Agriculture and Food Systems grant no. 01–52100–11346 to A.K., R.P.W., R.A.W., T.J.C., and G.J.M.; National Research Initiative grant nos. 99–35300–7694 to R.A.W., T.J.C., A.K., and R.P.W., 02–35300–12619 to J.A.D. and R.P.W., 02–35300–12548 to T.J.C., and 98–35300–6169 to R.P.W.; and Cooperative State Research, Education, and Extension Service North American Barley Genome Project funds to R.P.W. and D.A.A.).

* Corresponding author; e-mail rpwise{at}iastate.edu; fax 515–294–9420.

Received October 16, 2003; returned for revision November 25, 2003; accepted December 8, 2003.




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