Submitted to: The Plant Genome
Publication Type: Peer reviewed journal
Publication Acceptance Date: 9/29/2008
Publication Date: 11/21/2008
Citation: Tobias, C.M., Sarath, G., Twigg, P., Lindquist, E., Pangilinan, J., Penning, B., Barry, K., Carpita, N., Lazo, G.R. 2008. Comparative Genomics in Switchgrass Using 61,585 High-Quality EST. The Plant Genome. 1:111-124 Interpretive Summary: This work provides 'Kanlow' switchgrass sequence data from genes which are expressed in seedlings, crown tissue, and callus tissue. The sequences are highly similar to sorghum as well as other warm season grasses and can be used to help develop breeding and biotechnological approaches to switchgrass improvement. DNA-based markers were developed and tested for polymorphisms in two parental lines. These will allow development of a genetic map through screening the segregating progeny of these two parents. The sequence assembly was slightly more diverse than sorghum as judged though pairwise comparisons of related gene sequences within switchgrass. This may be a consequence of the high level of cross-pollination that is normal for this species.
Technical Abstract: Three cDNA libraries from callus, crown, and seedling tissues of switchgrass cv. Kanlow were end-sequenced to generate a total of 61,585 high quality reads from 36,565 separate clones. These were clustered and then assembled into consensus sequences and aligned with the sorghum genome when possible. Sixty-five percent of the ESTs were matched with gene ontology (GO) molecular terms and 3.3% of the sequences were matched with genes that play potential roles in cell-wall biogenesis. Amplification of EST-SSR markers on two individuals yielded an average of 2.18 amplicons per individual and 35% of the markers gave length polymorphisms. Conceptual translations of the assembled sequences using predicted coding sequences from sorghum as guides were created and pairwise comparisons of synonymous codon substitutions were made between similar sequences to globally assess sequence diversity. -