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John Vogel – Plant Functional Genomics

John Vogel

John Vogel, DOE Joint Genome Institute

John Vogel joined the DOE Joint Genome Institute in 2014 to establish a plant functional genomics research program. Prior to this, he served as a Research Molecular Biologist at the USDA for 12 years where he was a driving force behind the development of numerous genomic resources that fostered the widespread adoption of Brachypodium distachyon as an experimental model for the grasses. Major accomplishments in this context include: development of a high-efficiency transformation method, leading the international consortium that produced the reference genome sequence, the creation of 22,000 sequence-indexed insertional mutants (T-DNA lines), the assembly and characterization of the first large germplasm collection and the resequencing of 54 natural accessions. More recently, his research has expanded to include other Brachypodium species as models for polyploidy and perenniality. In addition to this fundamental work, he established an efficient switchgrass transformation pipeline and, in collaboration with industrial partners, generated hundreds of transgenic switchgrass lines in an effort to create improved varieties for biomass production. He did his postdoctoral studies with Shauna Somerville at the Carnegie Institution for Science where he studied the molecular basis of a plant host’s susceptibility to pathogens.

Education

  • BS in Plant Science, Cornell University, NY
  • PhD in Biology, University of Illinois at Chicago, IL

Research Interests

Dr. Vogel’s research is focused on developing plant functional genomic resources and utilizing these resources to understand genome organization and regulation, abiotic stress tolerance and the molecular basis of perenniality. Most projects in his lab utilize B. distachyon and related species as model systems to develop knowledge that will ultimately be used to improve biomass crops like switchgrass. Major projects currently underway include: 1) Using a trio of Brachypodium species as a model for polyploidy in order to understand polyploidy genome evolution and regulation 2) Determining the molecular mechanism of engineered resistance to multiple abiotic stresses and the molecular basis of perenniality using the perennial model grass Brachypodium sylvaticum 3) Developing a comprehensive collection of grass mutants by sequencing chemical and radiation induced mutants.

Select Publications

  1. 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
  2. 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
  3. 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 Biology14:25  doi:10.1186/1471-2229-14-25
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. Vogel, J., Hill, T. 2008 High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Rep. 27: 471-478.
  10. Vogel, J. 2008 Unique aspects of the grass cell wall. Current Opinion in Plant Biology. 11: 301-307
  11. Vogel, J., Garvin, D., Leong, O., and Hayden, D 2006 Agrobacterium-mediated transformation and inbred line development in the model grass Brachypodium distachyon. Plant Cell Tiss. and Organ Cult. 84:199-211