Theoretical and Applied Genetics

, Volume 111, Issue 5, pp 956–964

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

Authors

    • USDA, ARS, Western Regional Research CenterGenomics and Gene Discovery Unit
  • Paul Twigg
    • Biology Department, Bruner Hall of ScienceUniversity of Nebraska at Kearney
  • Daniel M. Hayden
    • USDA, ARS, Western Regional Research CenterGenomics and Gene Discovery Unit
  • Kenneth P. Vogel
    • USDA, ARS, Wheat, Sorghum and Forage Research Unit, Keim HallE.C. University of Nebraska
  • Rob M. Mitchell
    • USDA, ARS, Wheat, Sorghum and Forage Research Unit, Keim HallE.C. University of Nebraska
  • Gerard R. Lazo
    • USDA, ARS, Western Regional Research CenterGenomics and Gene Discovery Unit
  • Elaine K. Chow
    • USDA, ARS, Western Regional Research CenterGenomics and Gene Discovery Unit
  • Gautam Sarath
    • USDA, ARS, Wheat, Sorghum and Forage Research Unit, Keim HallE.C. University of Nebraska
Original Paper

DOI: 10.1007/s00122-005-0030-3

Cite this article as:
Tobias, C.M., Twigg, P., Hayden, D.M. et al. Theor Appl Genet (2005) 111: 956. doi:10.1007/s00122-005-0030-3

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.

Copyright information

© Springer-Verlag 2005