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First published online September 16, 2005; 10.1104/pp.105.066134

Plant Physiology 139:869-884 (2005)
© 2005 American Society of Plant Biologists

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GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Sorghum Expressed Sequence Tags Identify Signature Genes for Drought, Pathogenesis, and Skotomorphogenesis from a Milestone Set of 16,801 Unique Transcripts1,[w]

Lee H. Pratt*, Chun Liang, Manish Shah, Feng Sun, Haiming Wang, St. Patrick Reid2, Alan R. Gingle, Andrew H. Paterson, Rod Wing3, Ralph Dean4, Robert Klein, Henry T. Nguyen5, Hong-mei Ma, Xin Zhao, Daryl T. Morishige, John E. Mullet and Marie-Michèle Cordonnier-Pratt

Department of Plant Biology (L.H.P., C.L., M.S., F.S., H.W., S.P.R., M.-M.C.-P.), Center for Applied Genetic Technologies (A.R.G.), Plant Genome Mapping Laboratory (A.H.P., H.-m.M.), and Department of Statistics (X.Z.), University of Georgia, Athens, Georgia 30602; Clemson University Genomics Institute (R.W.) and Department of Plant Pathology and Physiology (R.D.), Clemson University, Clemson, South Carolina 29634; United States Department of Agriculture Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, Texas 77845 (R.K.); Department of Plant and Soil Sciences, Texas Tech University, Lubbock, Texas 79409 (H.T.N.); and Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843 (D.T.M., J.E.M.)

Improved knowledge of the sorghum transcriptome will enhance basic understanding of how plants respond to stresses and serve as a source of genes of value to agriculture. Toward this goal, Sorghum bicolor L. Moench cDNA libraries were prepared from light- and dark-grown seedlings, drought-stressed plants, Colletotrichum-infected seedlings and plants, ovaries, embryos, and immature panicles. Other libraries were prepared with meristems from Sorghum propinquum (Kunth) Hitchc. that had been photoperiodically induced to flower, and with rhizomes from S. propinquum and johnsongrass (Sorghum halepense L. Pers.). A total of 117,682 expressed sequence tags (ESTs) were obtained representing both 3' and 5' sequences from about half that number of cDNA clones. A total of 16,801 unique transcripts, representing tentative UniScripts (TUs), were identified from 55,783 3' ESTs. Of these TUs, 9,032 are represented by two or more ESTs. Collectively, these libraries were predicted to contain a total of approximately 31,000 TUs. Individual libraries, however, were predicted to contain no more than about 6,000 to 9,000, with the exception of light-grown seedlings, which yielded an estimate of close to 13,000. In addition, each library exhibits about the same level of complexity with respect to both the number of TUs preferentially expressed in that library and the frequency with which two or more ESTs is found in only that library. These results indicate that the sorghum genome is expressed in highly selective fashion in the individual organs and in response to the environmental conditions surveyed here. Close to 2,000 differentially expressed TUs were identified among the cDNA libraries examined, of which 775 were differentially expressed at a confidence level of 98%. From these 775 TUs, signature genes were identified defining drought, Colletotrichum infection, skotomorphogenesis (etiolation), ovary, immature panicle, and embryo.

1 This work was supported by the National Science Foundation Plant Genome Research Program (grant nos. DBI–9872649 to A.H.P. and DBI–0110140 to L.H.P.), by a gift from the National Grain Sorghum Producers, and by grants to H.T.N. from the Texas Advanced Technology Research Program and the U.S. Department of Agriculture National Research Initiative.

2 Present address: Department of Microbiology, Mount Sinai School of Medicine, 1 Gustave L. Levy Place, New York, NY 10029.

3 Present address: Arizona Genomics Institute and Department of Plant Sciences, University of Arizona, Tucson, AZ 85721.

4 Present address: Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC 27606.

5 Present address: Department of Agronomy, Plant Sciences Unit, University of Missouri, Columbia, MO 65211.

[w] The online version of this article contains Web-only data.

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.105.066134.

* Corresponding author; e-mail lpratt{at}plantbio.uga.edu; fax 706–583–0210.

Received May 27, 2005; returned for revision July 20, 2005; accepted July 26, 2005.




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