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Analysis of expressed sequence tags and the identification of associated short tandem repeats in switchgrass

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Abstract

Switchgrass is a large, North American, perennial grass that is being evaluated as a potential energy crop. Expressed sequence tags (ESTs) were generated from four switchgrass cv. “Kanlow” cDNA libraries to create a gene inventory of 7,810 unique gene clusters from a total of 11,990 individual sequences. Blast similarity searches to SwissProt and GenBank non-redundant protein and nucleotide databases were performed and a total of 79% of these unique clusters were found to be similar to existing protein or nucleotide sequences. Tentative functional classification of 61% of the sequences was possible by association with appropriate gene ontology descriptors. Significant differential representation between genes in leaf, stem, crown, and callus libraries was observed for many highly expressed genes The unique gene clusters were screened for the presence of short tandem repeats for further development as microsatellite markers. A total of 334 gene clusters contained repeats representing 3.8% of the ESTs queried.

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Acknowledgments

Supported by the United States Department of Agriculture, Agricultural Research Service CRIS 5325-21000-013-00, NP307 Biofuel and Bioenergy Alternatives. This work was also supported in part by NIH Grant P20 RR16569 from the BRIN Program of the National Center for Research Resources, and by a University of Nebraska at Kearney Research Services Council grant.

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Authors and Affiliations

  1. USDA, ARS, Western Regional Research Center, Genomics and Gene Discovery Unit, 800 Buchanan Street, Albany, CA, 94710, USA

    Christian M. Tobias, Daniel M. Hayden, Gerard R. Lazo & Elaine K. Chow

  2. Biology Department, Bruner Hall of Science, University of Nebraska at Kearney, Kearney, NE, 68849, USA

    Paul Twigg

  3. USDA, ARS, Wheat, Sorghum and Forage Research Unit, Keim Hall, E.C. University of Nebraska, Lincoln, NE, 68583, USA

    Kenneth P. Vogel, Rob M. Mitchell & Gautam Sarath

Authors
  1. Christian M. Tobias
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  2. Paul Twigg
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  3. Daniel M. Hayden
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  4. Kenneth P. Vogel
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  5. Rob M. Mitchell
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  6. Gerard R. Lazo
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  7. Elaine K. Chow
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  8. Gautam Sarath
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Correspondence to Christian M. Tobias.

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Communicated by T. Lübberstedt

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Tobias, C.M., Twigg, P., Hayden, D.M. et al. Analysis of expressed sequence tags and the identification of associated short tandem repeats in switchgrass. Theor Appl Genet 111, 956–964 (2005). https://doi.org/10.1007/s00122-005-0030-3

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  • DOI: https://doi.org/10.1007/s00122-005-0030-3

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