Brachypodium Resources

Welcome to the Brachypodium resource page of the Genomics and Gene Discovery Research Unit at the USDA-ARS Western Regional Research Center in Albany, CA, USA. Brachypodium distachyon (Brachypodium) is a small annual grass that is being developed as a model for the grasses in much the same way as Arabidopsis thaliana (Arabidopsis) has been developed as a model for dicotyledenous plants (dicots). Over the past several years we have put considerable effort into developing the tools necessary to use Brachypodium as a modern model organism. Some background information about Brachypodium may be found HERE. In order to aid researchers interested in using Brachypodium for in their laboratories, we have compiled a list of resources and methods we, along with collaborators, have developed over the past few years. We have also included a list of our publications that you may download as PDFs and links to other Brachypodium sites for even more information. We hope you find this information useful and if you have any questions feel free to contact us.

RESOURCES

T-DNA mutants: We are currently generating >7,500 T-DNA mutants as part of a DOE-funded grant. Here you can search for knockouts and order seeds (Additional T-DNA mutants can be found in the John Innes Collection).

Genome sequence: The entire Brachypodium genome has been sequenced and the assembly was of very high quality. We are currently working on a manuscript describing the genome sequencing project. The 8X genome assembly and the version 1.0 annotation is now available at: www.brachypodium.org, www.phytozome.org, and the MIPS Brachypodium site.

Resequencing Project: In addition to the reference genome sequence from Bd21, the Joint Genome Institute (JGI) has resequenced six other diploid inbred lines and an additional 50 more will be resequenced. Here you can find details about the project and instructions for nominating a line for resequencing.

Germplasm: In collaboration with colleagues from Turkey, we recently described over 200 new inbred lines. For more information please see our publication in BMC Plant Biology (Development of SSR markers and analysis of ...). Also see this TABLE of freely available germplasm.

High-density SNP map: We have created a genetic linkage map using a Bd21 X Bd3-1 mapping population created by David Garvin containing 562 markers. This map has been used to assemble the whole genome into chromosome scale assemblies (more details coming soon).

CMap viewer: We have loaded the final Brachypodium genome into the GrainGenes CMap viewing tool to enable comparative genomics. The sequence will be available soon.

Physical Map: See how the genome was put together using HICF BAC data.

METHODS

Publications

Fox, S.E., Preece, J., Kimbrel, J.A., Marchini, G.L., Sage, A., Youens-Clark, K., Cruzan, M.B., and Jaiswal, P. 2013. Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). Applications in Plant Sciences 1:1200011.

Wu, X., Wu, J., Luo, Y., Bragg, J., Vogel, J., and Gu, Y.Q. 2013. Phylogenetic, molecular, and biochemical characterization of caffeic aicd O-methyltransferase (COMT) gene family in Brachypodium distachyon. International Journal of Plant Genomics. 2013:423189.

Bragg, J.N., Wu, J., Gordon, S.P., Guttman, M.A., Thilmony, R.L., Lazo, G.R., Gu, Y.Q., and Vogel, J.P. 2012. Generation and Characterization of the Western Regional Research Center Brachypodium T-DNA Insertional Mutant Collection. PLoS ONE 7:e41916.

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., and Garvin, D.F. 2012. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS ONE 7:e38333

Chuck, G.S., Tobias, C., Sun, L., Kraemer, F., Li, C., Dibble, D., Arora, R., Bragg, J.N., Vogel, J.P., Singh, S., Simmons, B.A., Pauly, M., and Hake, S. 2011. Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass. Proc. Natl. Acad. Sci. 108:17550-17555.

Huo, N., Garvin, D.F., You, F.M., McMahon, S., Luo, M.C., Gu, Y.Q., Lazo, G.R., and Vogel, J.P. 2011. Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon. Theor. and Appl. Genet. 123:455-464.

"The International Brachypodium Initiative" 2010. Genome Sequencing and Analysis of The Model Grass Brachypodium distachyon. 2010. Nature 463:763-768.

Tyler, L., Bragg, J.N., Wu, J., Yang, X., Tuskan, G.A., and Vogel, J.P. 2010. Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. BMC Genomics. 11:600.

Filiz, E., Ozdemir, B.S., Budak, F., Vogel, J.P., Tuna, M., and Budak, H. 2009. Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome 52:876-890.

Garvin, D.F., McKenzie, N., Vogel, J.P., Mockler, T.C., Blankenheim, Z.J., Wright, J., Cheema, J.J.S., Dicks, J., Huo, N., Hayden, D.M., Gu, Y., Tobias, C., Chang, J.H., Chu, A., Trick, M., Michael, T.M., Bevan, M.W., and Snape, J.W. 2009. An SSR-based Genetic Linkage Map of the Model Grass Brachypodium distachyon. Genome 53:1-13.

Gu, Y.Q., Ma, Y., Huo, N., Vogel, J.P., You, F.M., Lazo, G.R., Nelson, W.M., Soderlund, C., Dvorak, J., and Luo, M.C. 2009. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics 10:496.

Vogel, J. P., Tuna, M., Budak, H., Huo, N., Gu, Y. Q., Steinwand, M. A. 2009. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biology 9:88.

Wei, B., Cai, T., Zhang, R., Li, A., Huo, N., Li, S., Gu, Y. Q., Vogel, J., Jia, J, Qi, Y., and Mao, L. 2009. Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Functional and Integrative Genomics 9:499-511.

Huo, N., Vogel, J., Lazo, G. R., You, F., Ma, Y., McMahon, S., Dvorak, J., Anderson, O., Luo, M., and Gu, Y. 2009. Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Molecular Biology 70:47.

Vogel, J., and Bragg, J. 2009. Brachypodium distachyon, a new model for the Triticeae. in: Genetics and Genomics of the Triticeae. Springer. 7:427-449.

Bortiri, E., Coleman-Derr, D., Lazo, G. R., Anderson, O. D., and Gu, Y. Q. 2008. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Research Notes 1:61. DOI:10.1186/1756-0500-1-61

Vogel, J., and Hill, T. 2008. High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Rep. 27:471-478.

Huo, N., Lazo, G. R., Vogel, J. P., You, F. M., Ma, Y., Hayden, D. M., Coleman-Derr, D., Hill, T. A., Dvorak, J, Anderson, O. D., Luo, M.-C., and Gu, Y. Q. 2008. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Functional and Integrative Genomics 8:135-147.

Vogel, J. 2008. Unique aspects of the grass cell wall. Current Opinion in Plant Biology 11:301-307.

Garvin, D., Gu, Y., Hasterok, R., Hazen, S., Jenkins, G., Mockler, T., Mur, L. J., and Vogel, J. P. 2008. Development of genetic and genomic research resources for Brachypodium distachyon, a new model for grass crop research. Crop Science 48:S69-S84.

Huo, N., Gu, Y., Lazo, G. R., Vogel, J., Coleman-Derr, D., Luo, M., Thilmony, R., Garvin, D., and Anderson, O. 2006. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome 49:1099-1108.

Vogel, J. P., Garvin, D. F., Leong, O. M., and Hayden, D. M. 2006. Agrobacterium-mediated transformation and inbred line development in the model grass Brachypodium distachyon. Plant Cell Tissue And Organ Culture 84:199-211.

Vogel, J. P., Gu, Y. Q., Twigg, P., Lazo, G. R., Chingcuanco, D. L., Hayden, D. M., Donze, T., Vivia-Lindsay, A., Stamova, B., and Coleman-Derr, D. 2006. EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. Theoretical and Applied Genetics 113:186-195.

Links to other Brachypodium distachyon Research Sites and Resources

The wEST resource is a USDA-ARS sponsored server of nucleic acid sequence data for Triticeae-associated research projects located at the USDA-ARS Western Regional Research Center, Albany, California. Other associated projects which use resources located at this site are:

E-mail inquiries to: curator@wheat.pw.usda.gov