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

Authors

Christian M. Tobias, USDA, ARSFollow
Paul Twigg, University of Nebraska at KearneyFollow
Daniel M. Hayden, USDA, ARS
Kenneth P. Vogel, University of Nebraska-LincolnFollow
Robert B. Mitchell, University of Nebraska-LincolnFollow
Gerard R. Lazo, USDA-ARS
Elaine K. Chow, USDA, ARS
Gautam Sarath, University of Nebraska-LincolnFollow

Document Type

Article

Date of this Version

9-2-2005

Comments

Published in Theor Appl Genet (2005) 111: 956–964.

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.