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Brachypodium Resources

Brachypodium distachyon is a small annual grass that researchers use as a model for the grasses used to produce biomass, food, feed and forage. Unlike the grasses grown as crops, B. distachyon is well suited to experimental manipulation in the laboratory because of its small size, compact genome, diploid nature, self compatibility, rapid generation time and simple growth requirements. In addition, numerous resources and methods (e.g. complete genome sequence, high efficiency transformation, large collections of natural accessions, many sequenced accessions and several RIL populations) are available that allow researchers to apply a suite of modern research methods to understand the unique aspects of grass biology. See here for a review of B. distachyon as a model system.

In addition to B. distachyon, other species in the genus are being used to study polyploidy (B. hybridum and B. stacei) and perenniality (B. sylvaticum).

Below are links to announcements and experimental resources and background information. If you have suggestions, please contact us.

Chemical and radiation mutants.

Announcements (updated 1-4-2017)

Let us know if you have an announcement

  • The website for the fourth International Brachypodium conference is now active: http://brachypodium2017.csp.escience.cn The conference will be held from July 29 to July 31, 2017 in Beijing, China. Key dates: February 1 registration opens; May 31 deadline for abstract submission; July 1 deadline for registration. Contact the organizer Zhiyong Liu with any questions.
  • T-DNA insertion sites have been updated to the v3 genome assembly and are available through the T-DNA page or through jbrowse in Phytozome.
  • The first book on Brachypodium genomics has been published.
  • The election for the International Brachypodium Steering Committee (IBSC) has been completed. Click here to view the results.
  • An improved reference genome assembly (v3.0) and annotation are now available on Phytozome.
  • The abstract book from the third International Brachypodium conference held 16-19 June 2015, in Amherst Massachusetts can be downloaded from the meeting website.

Resources and methods

T-DNA mutants

A collection of 23,649 T-DNA mutants is available.

Chemical and radiation mutants

A CSP project “Creating a genome-wide sequence-indexed collection of grass mutants” to sequence populations of EMS, fast neutron and sodium azide B. distachyon mutants was initiated in 2015. This project is a collaboration with researchers in France (Richard Sibout, INRA, IJPB) and the United States (Debbie Laudencia-Chingcuanco, USDA-ARS, WRRC). To date, over 270,000 mutations from 369 lines have been identified. When completed, this will be an unprecedented resource for forward and reverse genetics. If you would like to be involved in the screening or characterizing of this collection, please contact us.

Reference genome

An extremely high quality reference genome is available on Phytozome 11. Details of this highly improved assembly are available on Phytozome.

Germplasm

A large collection of inbred lines from geographically diverse locations has been established. A large collection of lines from Turkey are described in “Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon” and “Molecular, Morphological, and Cytological analysis of diverse B. distachyon inbred lines“. Most of the Turkish lines can be ordered from the National Plant Germplasm System. Many lines have been also been collected from Spain.

Garvin lab stocks including RIL populations.

Resequenced lines

Many natural accessions have been sequenced. Sequences for the first resequenced lines were published in 2014. De-novo assemblies have been created for 54 accessions and an additional 65 accessions are being sequenced by JGI. Download this spreadsheet for a complete list of sequenced lines and their statuses.

Protocols

Transformation:

Crossing:

EMS mutagensis:

Publications

Reviews

  • Brutnell TP, Bennetzen JL, Vogel JP. 2015 Brachypodium distachyon and Setaria viridis: model genetic systems for the grasses. Annu. Rev. Plant Biol. 66:In press. doi: 10.1146/annurev-arplant-042811-105528
  • Catalan P, Chalhoub B, Chochois V, Garvin DF, Hasterok R, Manzaneda AJ, Mur LAJ, Pecchioni N, Rasmussen SK, Vogel JP, Voxeur A 2014 Update on the genomics and basic biology of Brachypodium. Trends in Plant Science 19 (7), pp. 414-418
  • Chochois V, Vogel JP, Watt M 2012 Application of Brachypodium to the genetic improvement of wheat roots. J. of Exp. Bot. 63:3467-3474
  • Bragg, J. N., T. Ludmila and Vogel, J.P. 2012 Brachypodium distachyon, A Model for Bioenergy Grasses. Handbook of Bioenergy Crop Plants. Kole, C., Joshi, C.P. and Shonnard, D.R., Boca Rotan, Taylor & Francis Group. p 593-618
  • Brkljacic J, Grotewold E, Scholl R, Mockler T, Garvin DF, Vain P, Brutnell T, Sibout R, Bevan M, Budak H, Caicedo AL, Gao C, Gu Y, Hazen SP, Holt BF, Hong SY, Jordan M, Manzaneda AJ, Mitchell-Olds T, Mochida K, Mur LAJ, Park CM, Sedbrook J, Watt M, Zheng SJ, Vogel JP 2011 Brachypodium as a model for the grasses: Today and the future. Plant Phys. 157: 3-13
  • Mur LAJ, Allainguillaume J, Catalán P, Hasterok R, Jenkins G, Lesniewska K, Thomas I, Vogel J. 2011 Exploiting the Brachypodium tool box in cereal and grass research. New Phytologist 191: 334-347
  • 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
  • Vogel, J. P. and Bragg, J.N. 2009 Brachypodium distachyon, a New Model for the Triticeae. Genetics and Genomics of the Triticeae. Feuillet, C. and Muehlbauer, G. New York, Springer. 7: 427-449.
  • 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, LJ., and Vogel, JP.  2008 Development of genetic and genomic research resources for Brachypodium distachyon, a new model for grass crop research. Crop Science 48: S69-S84

Research papers

  • Rellán-Álvarez, R., Lobet, G., Lindner, H., Pradier, P., Sebastian, J., Yee, M., Geng, Y., Trontin, C., LaRue, T., Schrager-Lavelle, S., Haney, C.H., Nieu, R., Maloof, J., Vogel, J.P., José R Dinneny, J.R. 2015 GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. eLife 10.7554/eLife.07597 DOI: http://dx.doi.org/10.7554/eLife.07597
  • Chochois, V., Vogel, J.P., Rebetzke, G., and Watt, M. 2015 Variation in Adult Plant Phenotypes and Partitioning among Seed and Stem-Borne Roots across Brachypodium distachyon Accessions to Exploit in Breeding Cereals for Well-Watered and Drought Environments. Plant Physiology Vol. 168: 953-967
  • Bragg, N.B., Anderton, A., Nieu, R., and Vogel, J.P. 2015 Brachypodium distachyon. Agrobacterium Protocols: Volume 1 (Methods in Molecular Biology vol. 1223) Wang. K., New York, Springer. 2015, pp 17-33
  • Gordon, S.P., Priest, H., Des Marais, D.L., Schackwitz, W., Figueroa, M., Martin, J., Bragg, J.N., Tyler, L., Lee, C.R., Bryant, D., Wang, W., Messing, J., Manzaneda, A.J., Kerrie, B., Garvin, D.F., Budak, H., Tuna, M., Mitchell-Olds, T., Pfender, W.F., Juenger, T.E., Mockler, T.C., and Vogel, J.P., 2014 Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Inbred Lines 2014 Plant Journal 79: 361–374 DOI: 10.1111/tpj.12569
  • Poiré R., Chochois V., Sirault X.R.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 56 (8), pp. 781-796
  • Tyler L., Fangel J.U., Fagerström A.D., Steinwand M.A., Raab, T.K., Willats, W.G.T., Vogel, J.P. 2014 Selection and phenotypic characterization of a core collection of Brachypodium distachyon inbred lines BMC Plant Biology 14:25  doi:10.1186/1471-2229-14-25
  • O’Connor, D.L., Runions, A., Sluis, A., Bragg, J., Vogel, J.P., Prusinkiewicz, Hake, S. 2014 A Division in PIN-Mediated Auxin Patterning During Organ Initiation in Grasses PLoS Computational Biology DOI: 10.1371/journal.pcbi.1003447
  • Steinwand, M.A., Young, H.A., Bragg, J.N., Tobias, C.M., and Vogel, J.P. 2013 Brachypodium sylvaticum, a model for perennial grasses: transformation and inbred line development PLoS ONE 8(9): e75180. doi:10.1371/journal.pone.0075180
  • Wu, X., Wu, J., Luo, Y., Bragg, J., Vogel, J., Gu, Y.Q, 2013 Phylogenetic, Molecular, and Biochemical Characterization of Caffeic Acid o-Methyltransferase Gene Family in Brachypodium distachyon. International Journal of Plant Genomics 2013 Article ID 423189
  • Bragg, J.N., Wu, J., Gordon, S.P., Guttman, M.A., 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) art. no. 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., Garvin, D.F. 2012 Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS ONE 7 (6) art. no. 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., 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., 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
  • Tyler, L., Bragg, J.N., Wu, J., Yang, X., Tuskan, G.A., Vogel, J.P. 2010 Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. BMC Genomics. 11: 600
  • Vogel, J.P., Garvin, D.F., Mockler, T.C., Schmutz, J., Rokhsar, D., Bevan, M.W. et. al. (134 authors in total) 2010 Genome Sequencing and Analysis of The Model Grass Brachypodium distachyon. Nature. 463: 763-768
  • 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: Article No. 88
  • Gu, Y.Q., Ma, Y., Huo, N., Vogel, J.P., You, F.M., Lazo, G.R., Nelson, W.M., Soderlund, C., Dvorak, J., Luo, M.C. 2009 A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics 10:496.
  • 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.
  • 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.
  • Wei B., Cai T., Zhang R., Li A., Huo N., Li S., Gu Y.Q., Vogel J., Jia J, Qi Y., 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(4):499-511. 2009.
  • Huo, N., Vogel, J., Lazo, J., You, F., Ma, Y., McMahon, S., Dvorak, J., Anderson, O., Luo, M., and Gu, Y. 2008 Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Molecular Biology 70: 47
  • Vogel, J., 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., Vogel, J., You, F., Ma, Y., Hayden, D., Colemann-Derr, D., Hill, T., Dvorak, J., Anderson, O., Luo, M., Gu, Y. 2008 The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Functional and Integrative Genomics 8: 135-147
  • Huo, N., Gu, Y., Lazo, G., 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