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United States Department of Agriculture

Agricultural Research Service

Title: Construction and Evaluation of Cdna Libraries for Large Scale Est Sequencing in Wheat (Triticum Aestivum L.)

Authors
item Zhang, D - TEXAS TECH UNIV-LUBBOCK
item Choi, D - UNIV OF CA-RIVERSIDE
item Wanamaker, S - UNIV OF CA-RIVERSIDE
item Fenton, R - UNIV OF CA-RIVERSIDE
item Chin, A - UNIV OF CA-RIVERSIDE
item Malatrasi, M - UNIV OF CA-RIVERSIDE
item Turuspekov, Y - UNIV OF CA-RIVERSIDE
item Walia, H - UNIV OF CA-RIVERSIDE
item Akhunov, E - UNIV OF CALIFORNIA-DAVIS
item Kianian, P - NORTH DAKOTA STATE UNIV
item Otto, C - NORTH DAKOTA STATE UNIV
item Simons, K - NORTH DAKOTA STATE UNIV
item Deal, K - UNIV OF CALIFORNIA-DAVIS
item Echenique, V - UNIV OF CALIFORNIA-DAVIS
item Stamova, B - UNIV OF CALIFORNIA-DAVIS
item Ross, Kathleen
item Butler, E - UNIV OF ARIZONA-TUCSON
item Doherty, L - CENTRAL WA UNIV-ELLENSBUR
item Verhey, S - CENTRAL WA UNIV-ELLENSBUR
item Johnson, R - COLBY COLLEGE, MD
item Altenbach, Susan
item Kothari, Kerry
item Tanaka, Charlene
item Shah, M - UNIV OF NEBRASKA-LINCOLN
item L Chingcuanco, Debbie
item Gitt, Michael
item Pham, J - UNIV OF CALIFORNIA-DAVIS
item Han, P - UNIV OF CALIFORNIA-DAVIS
item Miller, R - UNIV OF CALIFORNIA-DAVIS
item Crossman, Curt
item Chao, Shiaoman
item Lazo, Gerard
item Klueva, N - TEXAS TECH UNIV-LUBBOCK
item Gustafson, J
item Kianian, S - NORTH DAKOTA STATE UNIV
item Dubcovsky, J - UNIV OF CALIFORNIA-DAVIS
item Walker-Simmons, M - CENTRAL WA UNIV-ELLENSBUR
item Gill, K - UNIV OF NEBRASKA-LINCOLN
item Dvorak, J - UNIV OF CALIFORNIA-DAVIS
item Anderson, Olin
item Mcguire, P - UNIV OF CALIFORNIA-DAVIS
item Qualset, C - UNIV OF CALIFORNIA-DAVIS
item Nguyen, H - TEXAS TECH UNIV-LUBBOCK
item Close, T - UNIV OF CA-RIVERSIDE

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 1, 2004
Publication Date: October 1, 2004
Citation: Zhang, D., Choi, D.W., Wanamaker, S., Fenton, R.D., Chin, A., Malatrasi, M., Turuspekov, Y., Walia, H., Akhunov, E., Kianian, P., Otto, C., Simons, K., Deal, K., Echenique, V., Stamova, B., Ross, K., Butler, E., Doherty, L., Verhey, S.D., Johnson, R., Altenbach, S.B., Kothari, K.M., Tanaka, C.K., Shah, M.M., Chingcuanco, D.L., Gitt, M.A., Pham, J., Han, P., Miller, R.E., Crossman, C.C., Chao, S., Lazo, G.R., Klueva, N., Gustafson, J.P., Kianian, S.F., Dubcovsky, J., Walker-Simmons, M.K., Gill, K.S., Dvorak, J., Anderson, O.D., Mcguire, P., Qualset, C.O., Nguyen, H.T., Close, T.J. 2004. Construction and evaluation of cdna libraries for large scale est sequencing in wheat (triticum aestivum l.). Genetics. 168:595-608.

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 library creation, materials, and methods. There were a total of 50 libraries that were created in wheat and related species. In general, the libraries were very good and produced over 101,345 sequences derived from 89,272 clones that defined 16,744 contigs and 33,202 singletons, for a sum total of 49,946 wheat 'unigenes.' It appears that many agronomically important wheat genes were characterized. This material is a unique resource available for comparative mapping, structural and functional analysis, and the study of polyploid evolution in wheat.

Technical Abstract: A total of 37 original cDNA libraries and nine libraries enriched for rare sequences were produced from Chinese Spring wheat (Triticum aestivum L.), five other hexaploid wheat genotypes (Cheyenne, Brevor, TAMW101, BH1146, and Butte 86), tetraploid durum wheat (Triticum turgidum L.), diploid wheat (Triticum monococcum L.), and two other diploid members of the tribe Triticeae (Aegilops speltoides Tausch. and Secale cereale L.). The emphasis in the choice of materials was reproductive development, including environmental factors that ultimately affect grain quality and yield, but efforts were made to also include roots and other sources of diverse gene representation. Partial cDNA 'expressed sequence tags' from these libraries were examined to assess the quality of these libraries by various measures. All sequences were processed to remove cloning system sequences and contaminants, then assembled using CAP3. Following these processing steps, a total of 101,345 sequences derived from 89,272 clones defined 16,744 contigs and 33,202 singletons, for a sum total of 49,946 'unigenes.' Analysis of the distribution of these unigenes among the various libraries led to the expected conclusion that the enrichment methods succeeded in reducing the most abundant unigenes, but also to the surprising observation that the most diverse libraries were made from tissues exposed to environmental stress including heat, drought, salinity, or low temperature.

Last Modified: 10/1/2014
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