Genetics, Vol. 168, 701-712, October 2004, Copyright © 2004
doi:10.1534/genetics.104.034868

A Chromosome Bin Map of 16,000 Expressed Sequence Tag Loci and Distribution of Genes Among the Three Genomes of Polyploid Wheat

L. L. Qi^*, B. Echalier^*, S. Chao^,1, G. R. Lazo, G. E. Butler, O. D. Anderson, E. D. Akhunov^¶, J. Dvoák^¶, A. M. Linkiewicz^¶,2, A. Ratnasiri^¶, J. Dubcovsky^¶, C. E. Bermudez-Kandianis^&, R. A. Greene^&, R. Kantety^&, C. M. La Rota^&, J. D. Munkvold^&, S. F. Sorrells^&, M. E. Sorrells^&, M. Dilbirligi^**, D. Sidhu^**, M. Erayman^**, H. S. Randhawa^**, D. Sandhu^**,3, S. N. Bondareva^**, K. S. Gill^**, A. A. Mahmoud, X.-F. Ma, Miftahudin, J. P. Gustafson, E. J. Conley, V. Nduati, J. L. Gonzalez-Hernandez^,4, J. A. Anderson, J. H. Peng^¶¶, N. L. V. Lapitan^¶¶, K. G. Hossain^&&, V. Kalavacharla^&&, S. F. Kianian^&&, M. S. Pathan, D. S. Zhang^***,5, H. T. Nguyen, D.-W. Choi^,6, R. D. Fenton, T. J. Close, P. E. McGuire, C. O. Qualset and B. S. Gill^*,7

^* Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, Kansas 66506-5502
Genetic Resources Conservation Program, University of California, Davis, California 95616
USDA-ARS Western Regional Research Center, Albany, California 94710
Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721
^¶ Department of Agronomy and Range Science, University of California, Davis, California 95616
^& Department of Plant Breeding, Cornell University, Ithaca, New York 14853
^** Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
Department of Agronomy, University of Missouri, Columbia, Missouri 65211
USDA-ARS Plant Genetics Research Unit, Department of Agronomy, University of Missouri, Columbia, Missouri 65211
Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
^¶¶ Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523-1170
^&& Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58105-5051
^*** Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79409
Department of Botany and Plant Sciences, University of California, Riverside, California 92521

⁷ Corresponding author: Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Throckmorton Hall, Manhattan, KS 66506-5502.
E-mail: bsg{at}ksu.edu

Because of the huge size of the common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) genome of 17,300 Mb, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids and deletion stocks. Each EST detected a mean of 4.8 restriction fragments and 2.8 loci. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general, EST density increased relative to the physical distance from the centromere. The majority of EST-dense regions are in the distal parts of chromosomes. Most of the agronomically important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.

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