Projects

THE HUNT FOR GREEN EVERY APRIL: FACTORS AFFECTING FITNESS IN SWITCHGRASS General Cooperative Agreement (A)   Accession Number: 418703

GENETIC FOUNDATIONS FOR BIOENERGY FEEDSTOCKS Appropriated (D)   Accession Number: 418493

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution - (Peer Reviewed Journal)

Melters, D.P., Bradnam, K.R., Young, H.P., Telis, N., May, M.R., Ruby, J., Sebra, R., Peluso, P., Eid, J., Rank, D., Garcia, J., Derisi, J.L., Smith, T.P., Tobias, C.M., Ross-Ibarra, J., Korf, I., Chan, S.W. 2013. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology. 14(1):R10. doi:10.1186/gb-2013-14-1-r10.

SNP discovery with EST and NextGen sequencing in switchgrass (panicum virgatum L.) - (Peer Reviewed Journal)

Ersoz, E.S., Wright, M.H., Pangilinan, J.L., Sheehan, M.J., Tobias, C.M., Casler, M.D., Buckler IV, E.S., Costich, D. 2012. SNP discovery with EST and NextGen sequencing in switchgrass (panicum virgatum L.). PLoS One. 7(9):e44112.

Switchgrass PviCAD1: Understanding residues important for substrate preferences and activity - (Peer Reviewed Journal) - (24-Apr-12)

Next generation sequencing of crown and rhizome transcriptome from an upland, tetraploid switchgrass - (Peer Reviewed Journal)

Palmer, N.A., Saathoff, A.J., Kim, J., Benson, A., Tobias, C.M., Twigg, P., Vogel, K.P., Madhavan, S., Sarath, G. 2012. Next generation sequencing of crown and rhizome transcriptome from an upland, tetraploid switchgrass. BioEnergy Research. 5:649-661. DOI 10.1007/s12155-011-9171-1.

The switchgrass genome: tools and strategies - (Peer Reviewed Journal)

Casler, M.D., Tobias, C.M., Kaeppler, S.M., Buell, R., Wang, Z., Cao, P., Ronald, P. 2011. The switchgrass genome: tools and strategies. The Plant Genome. 4:273-282.

Chloroplast genome variation in upland and lowland switchgrass - (Peer Reviewed Journal)

Young, H.A., Lanzatella-Craig, C., Sarath, G., Tobias, C.M. 2011. Chloroplast genome variation in upland and lowland switchgrass. PLoS One. 6(8): e23980. Available: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0023980.

DOWNREGULATION OF CINNAMYL-ALCOHOL DEHYDROGENASE IN SWITCHGRASS BY RNA SILENCING RESULTS IN ENHANCED GLUCOSE RELEASE AFTER CELLULASE TREATMENT - (Peer Reviewed Journal)

Saathoff, A.J., Sarath, G., Chow, E.K., Dien, B.S., Tobias, C.M. 2011. Downregulation of cinnamyl-alcohol dehydrogenase in switchgrass by RNA silencing results in enhanced glucose release after cellulase treatment. PLoS One. 6(1):e16416. DOI: 10.1371/journal.pone.0016416.

EM Algorithm for Mapping Quantitative Trait Loci in Multivalent Tetraploids - (Peer Reviewed Journal)

Li, J., Das, K., Fu, G., Lie, Y., Tobias, C.M., Wu, R. 2010. EM Algorithm for mapping quantitative trait loci in multivalent tetraploids. International Journal of Plant Genomics. Volume 2010 (2010), Article ID 216547. Available: http://www.hindawi.com/journals/ijpg/2010/216547/.

Hierarchical classification of switchgrass using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars - (Peer Reviewed Journal)

Zalapa, J., Price, D., Kaeppler, S., Tobias, C.M., Okada, M., Casler, M.D. 2010. Hierarchical classification of switchgrass using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars. Theoretical and Applied Genetics. 122:805-817.

Single-locus EST-SSR markers for characterization of population genetic diversity and structure across ploidy levels in switchgrass (Panicum virgatum L.) - (Peer Reviewed Journal) - (11-Oct-10)

Switchgrass contains two cinnamyl alcohol dehydrogenases involved in lignin formation - (Peer Reviewed Journal)

Saathoff, A.J., Tobias, C.M., Sattler, S.E., Haas, E.E., Twigg, P., Sarath, G. 2011. Switchgrass contains two cinnamyl alcohol dehydrogenases involved in lignin formation. BioEnergy Research. 4(2):120-133.

Biochemical and Genetic Characterization of Three Switchgrass CADs - (Abstract Only)

Saathoff, A.J., Tobias, C.M., Sattler, S.E., Haas, E.E., Twigg, P., Sarath, G. 2010. Biochemical and Genetic Characterization of Three Switchgrass CADs. Abstract only - presented at Biotechnology for Fuels and Chemicals Symposium Proceedings in Clearwater, FL, April 19-22, 2010. Not published elsewhere.

Discovering Traits Controlling Winter-hardiness and Spring Regrowth in Diverse Switchgrass Germplasm - (Abstract Only)

Sarath, G., Vogel, K.P., Tobias, C.M., Soundararajan, M., Twigg, P., Saathoff, A.J., Okada, M. 2010. Discovering Traits Controlling Winter-hardiness and Spring Regrowth in Diverse Switchgrass Germplasm. Abstract presented at Biotechnology for Fuels and Chemicals Symposium Proceedings April 19-22, 2010 in Clearwater, FL. Not published anywhere else.

COMPLETE SWITCHGRASS GENETIC MAPS REVEAL SUBGENOME COLLINEARITY, PREFERENTIAL PAIRING, AND MULTILOCUS INTERACTIONS - (Peer Reviewed Journal)

Okada, M., Lanzatella-Craig, C., Saha, M., Bouton, J., Wu, R., Tobias, C.M. 2010. Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions. Genetics. 185:745-760.

EST-SSR Markers Discriminate Switchgrass Ecotypes - (Abstract Only)

Zalapa, J., Casler, M.D., Kaeppler, S., De Leon, N., Tobias, C.M. 2010. EST-SSR Markers Discriminate Switchgrass Ecotypes. 2010 Genomic Science Contractor-Grantee and Knowledgebase Workshop. Available: www.orau.gov/gtl2010/postedabstracts.htm

Dihaploid stocks for switchgrass isolated by a screening approach - (Peer Reviewed Journal)

Young, H.A., Hernlem, B.J., Anderton, A.L., Lanzatella-Craig, C., Tobias, C.M. 2010. Dihaploid stocks for switchgrass isolated by a screening approach. BioEnergy Research. 3:305-313.

An SSR-Based Genetic Linkage Map of the Model Grass Brachypodium distachyon - (Peer Reviewed Journal)

Garvin, D.F., Mckenzie, N., Vogel, J.P., Mockler, T.C., Blankenheim, Z., Wright, J., Huo, N., Cheema, J.J., Dicks, J., Hayden, D.M., Gu, Y.Q., Tobias, C.M., Chang, J.H., Chu, A., Trick, M., Michael, T.P., Bevan, M.W., Snape, J.W. 2010. An SSR-Based Genetic Linkage Map of the Model Grass Brachypodium distachyon. Genome. 53(1):1-13.

A GENOME MAY REDUCE YOUR CARBON FOOTPRINT - (Review Article)

Tobias, C.M. 2009. A GENOME MAY REDUCE YOUR CARBON FOOTPRINT. The Plant Genome. 2:5-8.

Impact of Divergent Selection on the Abundance and Activities of Lignin Biosynthetic Enzymes in Switchgrass, and Characterization of Recombinant Switchgrass CAD and COMT Proteins - (Abstract Only)

Saathoff, A.J., Palmer, N.A., Tobias, C.M., Twigg, P., Sattler, S.E., Haas, E.J., Mitchell, R., Vogel, K.P., Sarath, G. 2009. Impact of Divergent Selection on the Abundance and Activities of Lignin Biosynthetic Enzymes in Switchgrass, and Characterization of Recombinant Switchgrass CAD and COMT Proteins. p. 47 Abstracts 31st Symposium on Biotechnology for Fuels and Chemicals, Soc. for Industrial Microbiology. May 3-6, 2009, San Francisco, CA.

Comparative Genomes in Switchgrass Using 61,585 High-Quality EST - (Peer Reviewed Journal)

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

GENIC MICROSATELLITE MARKERS DERIVED FROM EST SEQUENCES OF SWITCHGRASS (PANICUM VIRGATUM L.) - (Peer Reviewed Journal)

Tobias, C.M., Hayden, D.M., Twigg, P., Sarath, G. 2006. Genic microsatellite markers derived from EST sequences of switchgrass (Panicum virgatum L.). 6:185-187. Molecular Ecology Notes.

ANALYSIS OF EXPRESSED SEQUENCE TAGS AND THE IDENTIFICATION OF ASSOCIATED SHORT TANDEM REPEATS IN SWITCHGRASS - (Peer Reviewed Journal)

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.

APPLICATION OF FUNCTIONAL GENOMIC TOOLS FOR EXPLORING SWITCHGRASS FEEDSTOCKS IMPROVED THROUGH DIVERGENT SELECTION - (Abstract Only)

Sarath, G., Vogel, K.P., Mitchell, R., Twigg, P., Tobias, C.M., Baird, L.M. 2005. Application of functional genomic tools for exploring switchgrass feedstocks improved through divergent selection. Biotechnology for Fuels and Chemicals Symposium Proceedings.#3A-01.

STRUCTURE OF THE CINNAMYL-ALCOHOL DEHYDROGENASE GENE FAMILY IN RICE AND PROMOTER ACTIVITY OF A MEMBER ASSOCIATED WITH LIGNIFICATION. - (Peer Reviewed Journal)

Tobias, C.M., Chow, E.K. 2004. Structure of the Cinnamyl-Alcohol Dehydrogenase Gene Family in Rice and Promoter Activity of a Member Associated with Lignification. Planta. 220:678-688.