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United States Department of Agriculture

Agricultural Research Service

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
item Edwards, H
item Crossman, Curt
item Lui, N
item Matthews, D
item Blake, Victoria
item Hane, D
item You, F
item Butler, E
item Miller, R
item Close, T
item Peng, J
item Lapitan, N l
item Gustafson, J
item Qi, L
item Echalier, B
item Gill, B
item Dilbirligi, M
item Sandhu, D
item Gill, K
item Greene, R
item Sorrells, M
item Akhunov, E
item Dvorak, J
item Linkiewicz, A
item Dubcovsky, J
item Hossain, K
item Kianian, S
item Mahmoud, A
item Miftahudin,
item Ma, Xeufeng
item Wennerlind, E
item Anderson, J
item Pathan, M
item Nguyen, H
item Mcguire, P
item Qualset, C
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.

Last Modified: 8/24/2016
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