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Genetics, Vol. 168, 585-593, October 2004, Copyright © 2004
doi:10.1534/genetics.104.034777

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Development of an Expressed Sequence Tag (EST) Resource for Wheat (Triticum aestivum L.)

EST Generation, Unigene Analysis, Probe Selection and Bioinformatics for a 16,000-Locus Bin-Delineated Map

G. R. Lazo*,1, S. Chao{dagger},1,2, D. D. Hummel{dagger}, H. Edwards{dagger}, C. C. Crossman*, N. Lui{dagger}, D. E. Matthews*,{ddagger}, V. L. Carollo*, D. L. Hane{dagger}, F. M. You§, G. E. Butler, R. E. Miller{dagger}, T. J. Close&, J. H. Peng**, N. L. V. Lapitan**, J. P. Gustafson{dagger}{dagger}, L. L. Qi{ddagger}{ddagger}, B. Echalier{ddagger}{ddagger}, B. S. Gill{ddagger}{ddagger}, M. Dilbirligi§§, H. S. Randhawa§§,3, K. S. Gill§§, R. A. Greene{dagger}, M. E. Sorrells{dagger}, E. D. Akhunov§, J. Dvorák§, A. M. Linkiewicz§,4, J. Dubcovsky§, K. G. Hossain¶¶, V. Kalavacharla¶¶, S. F. Kianian¶¶, A. A. Mahmoud&&, Miftahudin***, X.-F. Ma***, E. J. Conley&&, J. A. Anderson&&, M. S. Pathan***, H. T. Nguyen***, P. E. McGuire{dagger}, C. O. Qualset{dagger} and O. D. Anderson*,5

* U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Western Regional Research Center, Albany, California 94710-1105
{dagger} Genetic Resources Conservation Program, University of California, Davis, California 95616
{ddagger} Department of Plant Breeding, Cornell University, Ithaca, New York 14853
§ Department of Agronomy and Range Science, University of California, Davis, California 95616
Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721
& Department of Botany and Plant Sciences, University of California, Riverside, California, 92521
** Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170
{dagger}{dagger} USDA-ARS Plant Genetics Research Unit, Department of Agronomy, University of Missouri, Columbia, Missouri 65211
{ddagger}{ddagger} Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, Kansas 66506-5502
§§ Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
¶¶ Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58105
*** Department of Agronomy, University of Missouri, Columbia, Missouri 65211
&& Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108

5 Corresponding author: USDA-ARS-WRRC, 800 Buchanan St., Albany, CA 94710-1105.
E-mail: oandersn{at}pw.usda.gov

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid (2n = 6x = 42) wheat genome (Triticum aestivum L.). Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags (ESTs) representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection (113,220 ESTs). Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of ESTs into contigs. These contigs plus singletons (unassembled ESTs) were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5' and 3' sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics.




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