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Title: 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

Author
item Lazo, Gerard
item Chao, Shiaoman
item HUMMEL, D - UNIV OF CALIFORNIA-DAVIS
item EDWARDS, H - CORNELL UNIVERSITY
item Crossman, Curt
item LUI, N - UNIV OF CALIFORNIA-DAVIS
item MATTHEWS, D - CORNELL UNIVERSITY
item Blake, Victoria
item HANE, D - UNIV OF CALIFORNIA-DAVIS
item YOU, F - UNIV OF CALIFORNIA-DAVIS
item BUTLER, E - CORNELL UNIVERSITY
item MILLER, R - UNIV OF CALIFORNIA-DAVIS
item CLOSE, T - UNIV OF CA-RIVERSIDE
item PENG, J - COLORADO STATE UNIV
item LAPITAN, N L - COLORADO STATE UNIV
item Gustafson, J
item QI, L - KANSAS STATE UNIVERSITY
item ECHALIER, B - KANSAS STATE UNIVERSITY
item GILL, B - KANSAS STATE UNIVERSITY
item DILBIRLIGI, M - WASHINGTON STATE UNIV
item SANDHU, D - WASHINGTON STATE UNIV
item GILL, K - WASHINGTON STATE UNIV
item GREENE, R - CORNELL UNIVERSITY
item SORRELLS, M - CORNELL UNIVERSITY
item AKHUNOV, E - UNIV OF CALIFORNIA-DAVIS
item DVORAK, J - UNIV OF CALIFORNIA-DAVIS
item LINKIEWICZ, A - UNIV OF CALIFORNIA-DAVIS
item DUBCOVSKY, J - UNIV OF CALIFORNIA-DAVIS
item HOSSAIN, K - NORTH DAKOTA STATE UNIV
item KIANIAN, S - NORTH DAKOTA STATE UNIV
item MAHMOUD, A - UNIV OF MISSOURI-COLUMBIA
item MIFTAHUDIN - UNIV OF MISSOURI-COLUMBIA
item MA, XEUFENG - UNIV OF MISSOURI-COLUMBIA
item WENNERLIND, E - UNIV OF MINNESOTA-ST PAUL
item ANDERSON, J - UNIV OF MINNESOTA-ST PAUL
item PATHAN, M - UNIV OF MISSOURI-COLUMBIA
item NGUYEN, H - UNIV OF MISSOURI-COLUMBIA
item MCGUIRE, P - UNIV OF CALIFORNIA-DAVIS
item QUALSET, C - UNIV OF CALIFORNIA-DAVIS
item Anderson, Olin

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2004
Publication Date: 10/7/2004
Citation: Lazo, G.R., Chao, S., Hummel, D.H., Edwards, H., Crossman, C.C., Lui, N., Matthews, D.E., Carollo, V.L., Hane, D., You, F.M., Butler, E., Miller, R., Close, T.J., Peng, J., Lapitan, N.V., Gustafson, J.P., Qi, L.L., Echalier, B., Gill, B.S., Dilbirligi, M., Sandhu, D., Gill, K.S., Greene, R.A., Sorrells, M.E., Akhunov, E.D., Dvorak, J., Linkiewicz, A.M., Dubcovsky, J., Hossain, K.G., Kianian, S.F., Mahmoud, A., Miftahudin, Ma, X., Wennerlind, E.J., Anderson, J.A., Pathan, M.S., Nguyen, H.T., Mcguire, P.E., Qualset, C.O., Anderson, O.D. 2004. 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. Genetics. 168:585-593.

Interpretive Summary: The hexaploid wheat genome is about 17,300 Mb in size, which makes mapping of the expressed portion, the first step in looking for gene discovery, a monumental task. We report on the introduction, library creation, materials, and methods for the mapping of 7,104 expressed sequence tags (EST) into chromosome deletion bin maps. The EST density was higher depending on the particular region of the hexaploid wheat genome. In general, EST density increased relative to the physical distance from the middle of individual wheat chromosomes. It appears that most of the agronomically important genes are located in these EST-dense regions. The chromosome bin map of ESTs is a unique resource for comparative mapping, structural and functional analysis, and the study of polyploid evolution in wheat.

Technical Abstract: A bin map of the hexaploid wheat genome was constructed using a 117,510-member, wheat EST resource and a germplasm deletion series that allowed restriction fragment localization to chromosome deletions without the necessity of polymorphisms. This report describes the development of the first extensive wheat EST collection, including protocols for sequencing, sequence processing, and EST nomenclature. The ESTs were assembled into contigs, and the contigs plus singletons (un-assembled ESTs) used for selection of unigenes probes. Selected ESTs were rearrayed, validated by 5' and 3' sequencing, and inserts amplified for probing the series of wheat aneuploid stocks missing either entire chromosomes or specific chromosome arms. Provisions for validating map positions that utilized web pages for project communication and coordination are described. Project data were deposited in accessible databases, and examples are shown of a web-based access point for data from this and related projects, for queries for probes, for contig and map details, and linkage of project data to external databases.