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

Christian M. Tobias, Paul Twigg, Daniel M. Hayden, Kenneth P. Vogel, Rob M. Mitchell, Gerard R. Lazo, Elaine K. Chow, Gautam Sarath

Research output: Contribution to journalArticle

46 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)956-964
Number of pages9
JournalTheoretical and Applied Genetics
Volume111
Issue number5
DOIs
StatePublished - Sep 1 2005

Fingerprint

Panicum
Panicum virgatum
Expressed Sequence Tags
Multigene Family
expressed sequence tags
Microsatellite Repeats
Protein Databases
multigene family
microsatellite repeats
Genes
Gene Ontology
genes
Nucleic Acid Databases
Bony Callus
Poaceae
Crowns
Gene Library
root crown
energy crops
Nucleotides

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Genetics

Cite this

Analysis of expressed sequence tags and the identification of associated short tandem repeats in switchgrass. / Tobias, Christian M.; Twigg, Paul; Hayden, Daniel M.; Vogel, Kenneth P.; Mitchell, Rob M.; Lazo, Gerard R.; Chow, Elaine K.; Sarath, Gautam.

In: Theoretical and Applied Genetics, Vol. 111, No. 5, 01.09.2005, p. 956-964.

Research output: Contribution to journalArticle

Tobias, Christian M. ; Twigg, Paul ; Hayden, Daniel M. ; Vogel, Kenneth P. ; Mitchell, Rob M. ; Lazo, Gerard R. ; Chow, Elaine K. ; Sarath, Gautam. / Analysis of expressed sequence tags and the identification of associated short tandem repeats in switchgrass. In: Theoretical and Applied Genetics. 2005 ; Vol. 111, No. 5. pp. 956-964.
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