ARS | Publication request: ANALYSIS OF EXPRESSED SEQUENCE TAGS AND THE IDENTIFICATION OF ASSOCIATED SHORT TANDEM REPEATS IN SWITCHGRASS

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 19, 2005
Publication Date: July 28, 2005
Citation: Tobias, C.M., Twigg, P., Hayden, D.M., Vogel, K.P., Mitchell, R., Lazo, G.R., Chow, E.K., Sarath, G. 2005. Analysis of expressed sequence tags and the identification of associated short tandem repeats in switchgrass. Theoretical and Applied Genetics. 111: 956-964.

Interpretive Summary: Application of molecular approaches to plant-based biomass production in dedicated energy crops has only recently begun. Ultimately these approaches may improve yields, direct synthesis of valuable co-products, or reduce conversion costs. Achievement of these goals would improve the economies of biomass production and conversion that have in the past limited its utilization. Switchgrass is a high yielding, C4, perennial grass component of the North American tall grass prairie that once occupied a large portion of the continental United States. It has been cofired with coal in power plants but it also has excellent potential as a feedstock for ethanol production with yields estimated to be from 4400-5600 liters ha-1. An enhanced understanding of cell wall biogenesis at the molecular level in switchgrass may lead to new approaches to enhance feedstock quality for this end use. Marker development will also allow more efficient breeding approaches to be adopted. We have generated sequence information from the expressed portion of the switchgrass genome that will be useful for both of these goals.

Technical 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 7810 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.