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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Foundations for Bioenergy Feedstocks Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines - (Peer Reviewed Journal)
Gordon, S.P., Priest, H., Des Marais, D., Schackwitz, W., Figueroa, M., Martin, J., Bragg, J., Tyler, L., Lee, C., Bryant, D., Wang, W., Messing, J., Manzaneda, A., Barry, K., Garvin, D.F., Budak, H., Tuna, M., Mitchell-Olds, T., Pfender, W.F., Juenger, T., Mockler, T., Vogel, J.P. 2014. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant Journal. 79:361-374.
Whole plant phenotypic variability in nitrogen and phosphorus response of Brachypodium distachyon - (Peer Reviewed Journal)
Poire, R.R., Chohois, V., Sirault, X.R., Vogel, J.P., Watt, M., Furbank, R.T. 2014. Whole plant phenotypic variability in nitrogen and phosphorus response of Brachypodium distachyon. Journal of Integrative Plant Biology. DOI: 10.1111/jipb.12198.
Genetic Linkage Mapping and Segregation Distortion in a Three-Generation Four-Founder Population of Panicum vigatum (L.) - (Peer Reviewed Journal)
Li, G., Serba, D.D., Saha, M.C., Bouton, J.H., Lanzatella-Craig, C., Tobias, C.M. 2014. Genetic Linkage Mapping and Segregation Distortion in a Three-Generation Four-Founder Population of Panicum vigatum (L.). Genes, Genomes, and Genomics. DOI: 10.1534/g3.113.010165.
Selection and phenotypic characterization of a core collection of Brachypodium distachyon inbred lines. - (Peer Reviewed Journal)
Tyler, L., Fangel, J.U., Fagerstrom, A.D., Steinwand, M., Raab, T.K., Willats, W.G., Vogel, J.P. 2014. Phenotypic diversity in a core collection of Brachypodium distachyon inbred lines. Biomed Central (BMC) Plant Biology. 14:25.
A statistical model for QTL mapping in polysomic autotetraploids underlying double reduction - (Peer Reviewed Journal)
Xu, F., Lyu, Y., Tong, C., Wu, W., Zhu, X., Yin, D., Yan, Q., Zhang, J., Pang, X., Tobias, C.M., Wu, R. 2013. A statistical model for QTL mapping in polysomic autotetraploids underlying double reduction. Briefings in Bioinformatics. DOI: 10.1093/bib/bbt073.
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution - (Peer Reviewed Journal)
Melters, D.P., Bradnan, K., Young, H., Telis, N., May, M., Ruby, G.J., Sebra, R., Peluso, P., Eid, J., Rank, D., Garcia, J., Derisi, J., Smith, T.P., Tobias, C.M., Ross-Ibarra, J., Korf, I., Chan-Simon, W. 2013. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology. doi:10.1186/gb-2013-14-1-r10.
Switchgrass Genomics - (Book / Chapter)
Tobias, C.M. 2013. Switchgrass Genomics. Bioenergy Feedstocks: Breeding and Genetics. 1:33-48.
A multivalent three-point linkage analysis model of autotetraploids - (Peer Reviewed Journal)
Lu, Y., Yang, X., Tong, C., Li, X., Feng, S., Wang, Z., Pang, X., Wang, Y., Wang, N., Tobias, C.M., Wu, R. 2012. A multivalent three-point linkage analysis model of autotetraploids. Briefings in Bioinformatics. doi:10.1093/bib/bbs051.
Karyotype variation is indicative of subgenomic and ecotypic differentiation in switchgrass - (Peer Reviewed Journal)
Young, H., Sarath, G., Tobias, C.M. 2012. Karyotype variation is indicative of subgenomic and ecotypic differentiation in switchgrass. Biomed Central (BMC) Plant Biology. 12:117.
Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection - (Peer Reviewed Journal)
Bragg, J., Wu, J., Gordon, S.P., Guttman, M.E., Thilmony, R.L., Lazo, G.R., Gu, Y.Q., Vogel, J.P. 2012. Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection. PLoS One. 7(9):e41916. doi:10.1371/journal.pone.0041916.
Fine mapping of the Bsrl barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. - (Peer Reviewed Journal)
Cui, Y., Lee, M.Y., Huo, N., Bragg, J., Yan, L., Yuan, C., Li, C., Holditch, S.J., Xie, J., Luo, M.C., Li, D., Yu, J., Martin, J., Schackwitz, W., Gu, Y.Q., Vogel, J.P., Jackson, A.O., Liu, Z., Garvin, D.F. 2012. Fine mapping of the Bsrl barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One. 7:e38333.
A unifying framework for bivalent multilocus linkage analysis of allotetraploids - (Peer Reviewed Journal)
Yang, X., Lu, Y., Pang, X., Tong, C., Wang, Z., Li, X., Feng, S., Tobias, C.M., Wu, R. 2012. A unifying framework for bivalent multilocus linkage analysis of allotetraploids. Briefings in Bioinformatics. 14:96-108.
Application of Brachypodium to the genetic improvement of wheat roots - (Review Article)
Chochois, V., Vogel, J.P., Watt, M. 2012. Application of Brachypodium to the genetic improvement of wheat roots. Journal of Experimental Botany. 63:3467-3474.
Chloroplast genome variation in upland and lowland switchgrass     Reprint Icon - (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.
Incorporation of high-molecular-weight glutenin subunits into doughs using 2 gram mixograph and extensigraphs - (Peer Reviewed Journal)
Anderson, O.D., Bekes, F. 2011. Incorporation of high-molecular-weight glutenin subunits into doughs using 2 gram mixograph and extensigraphs. Journal of Cereal Science. 54:288.
Exploiting the Brachypodium Tool Box in cereal and grass research - (Review Article)
Mur, L., Allainguillaume, J., Catalan, P., Hasaterok, R., Jenkins, G., Lesniewski, K., Thomas, I., Vogel, J.P. 2011. Exploiting the Brachypodium tool box in cereal and grass research. New Phytologist. DOI: 10.1111/j.1469-8137.2011.03748.x.
Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon - (Peer Reviewed Journal)
Huo, N., Garvin, D.F., You, F., McMahon, S.A., Luo, M., Gu, Y.Q., Lazo, G.R., Vogel, J.P. 2011. Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon. Theoretical and Applied Genetics. 123(3):455-464.
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/.
Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon - (Peer Reviewed Journal)
Tyler, L., Bragg, J.N., Wu, J., Yng, X., Tuskan, G., Vogel, J.P. 2010. Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. Biomed Central (BMC) Genomics. 11:600.
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)
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.
Brachypodium distachyon genomics for sustainable food and fuel production - (Review Article)
Bevan, M.W., Garvin, D.F., Vogel, J.P. 2010. Brachypodium distachyon genomics for sustainable food and fuel production. Current Opinion in Biotechnology. 21:211-217.
Last Modified: 10/21/2014
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