Jeffrey Bennetzen
Norman and Doris Giles Professor and Georgia Research Alliance Eminent Scholar
Ph.D. (1980) University of Washington
Phone: 706-542-3698
Email: maize@uga.edu
See my Laboratory Home Page

Research Interests
My lab is interested in plant genome structure and evolution, especially the nature of rearrangements and the contributions of transposable elements. We also study the relationship between genome structure, evolution and gene function, particularly the identification of changes in regulatory genes that significantly differentiate species. We have a long-standing interests in genetic diversity and its use in under-utilized crops of the developing world, the rapid evolution of complex disease resistance loci in plants, the fine structure recombinational analysis, particularly within tandem gene families, and the coevolution of plant/microbe and plant/parasite interactions, primarily in the soil.

  • Ammiraju, J.S.S., F. Lu, A. Sanyal, Y. Yu, X. Song, N. Jiang, A.C. Pontaroli, T. Rambo, J. Currie, K. Collura, J. Talag, C. Fan, J.L. Goicoechea, A. Zuccolo, J.L. Bennetzen, M. Chen, S. Jackson and R.A. Wing. 2008. Dynamic evolution of Oryza genomes revealed by comparative genomic analysis of a genus-wide vertical dataset. Plant Cell, in press, published on line.
  • Nelson, W.M., M. Luo, J. Ma, M. Estep, J. Estill, R. He, J. Talag, N. Cisneros, D. Kudrna, H. Kim, J.S.S. Ammiraju, K. Collura, A.K. Bharti, J. Messing, R.A. Wing, P. SanMiguel, J.L. Bennetzen and C. Soderlund. 2008. Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains. BMC Genomics, in press, published on line.
  • Baucom, R.S., J.C. Estill, J. Leebans-Mack and J.L. Bennetzen. 2008. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res., in press, published on line.
  • Nagy, E.D. and J.L. Bennetzen. 2008. Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster. Genome Res. 18: 1918-1923.
  • Dida, M.M., N. Wanyera, M.L. Harrison Dunn, J.L. Bennetzen and K.M. Devos. 2008. Population structure and diversity in finger millet (Eleusine coracana) germplasm. Tropical Plant Biol. 1: 131-141.
  • Conner, J.A., S. Goel, G. Gunawan, M.-M. Cordonnier-Pratt, V.E. Johnson, C. Liang, H. Wang, L.H. Pratt, J.E. Mullet, J. DeBarry, L. Yang, J.L. Bennetzen, P.E. Klein and P. Ozias-Akins. 2008. Sequence analysis of BAC clones from the apospory-specific genomic regions (ASGR) of Pennisetum and Cenchrus. Plant Physiol. 147: 1396-1411.
  • DeBarry, J., R. Liu, and J.L. Bennetzen. 2008. Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. BMC Bioinformatics 9: 235.
  • Rensing, S.A. and many others, including J.L. Bennetzen. 2008. The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants. Science 319: 64-69.
  • Gorantla, M., P.R. Babu, W.V. Reddy Lachagari, A.M.M. Reddy, R. Wusirika, J.L. Bennetzen and A.R. Reddy. 2007. Identification of stress responsive genes in an indica rice (Oryza sativa L. cv. Nagina 22) using ESTs generated from drought stressed seedlings. J. Experimental Bot. 58: 253-265.
  • Dida, M., S. Srinivasachary, S. Ramakrishnan, J. Bennetzen, M. Gale, and K. Devos. 2007. The genetic map of finger millet, Eleusine coracana. Theor. Appl. Genet. 114: 321-332.
  • Nagy, E.D., T.-S. Lee, W. Ramakrishna, Z. Xu, P.E. Klein, P. SanMiguel, C.-P. Cheng, J. Li, K.M. Devos, K. Schertz, L. Dunkle and J. L. Bennetzen. 2007. Fine mapping of the Pc locus of Sorghum bicolor, a gene controlling the reaction of a fungal pathogen and its host-selective toxin. Theor. Appl. Genet. 114: 961-970.
  • Corby-Harris, V., A.C. Pontaroli, K.E. Habel, J.L. Bennetzen, L.J. Shimkets and D.E.L. Promislow. 2007. The geographical distribution and diversity of microbes in natural populations of Drosophila melanogaster. Appl. Environ. Microbiol. 73: 3470-3479.
  • Ma, J., R.A. Wing, J.L. Bennetzen, and S.A. Jackson. 2007. Plant centromere organization: conserved functions within a dynamic structure. Trends Genet. 123: 134-139.
  • Liu, R., C. Vitte, J. Ma, A.A. Mahama, T. Dhliwayo, M. Lee and J.L. Bennetzen. 2007. A GeneTrek analysis of the maize genome. Proc. Natl. Acad. Sci. USA 104: 11844-11849.
  • Ma, J., R.A. Wing, J.L. Bennetzen and S.A. Jackson. 2007. Evolutionary history and positional shift of a rice centromere. Genetics 177: 1217-1220.
  • Wicker, T., F. Sabot, A. Hua-Van, J.L. Bennetzen, P. Capy, B. Chaloub, A. Flavell, P. Leroy, M. Morgante, O. Panaud, E. Paux, P. SanMiguel, and A. Schulman. 2007. A unified classification system for eukaryotic transposable elements. Nature Rev. Genet. 8: 973-982.
  • Bennetzen, J.L. 2007. Patterns in grass genome evolution. Curr. Opin. Plant Biol. 10: 176-181.
  • Chu, Z., B. Fu, H. Yang, C. Xu, Z. Li, A. Sanchez, Y.J. Park, J.L. Bennetzen and S. Wang. 2006. Targeting xa13, a recessive gene for bacterial blight resistance in rice. Theor. Appl. Genet., 112: 455-461.
  • Ma, J. and J. L. Bennetzen. 2006. Recombination, rearrangement, reshuffling and divergence in a centromeric region of rice. Proc. Natl. Acad. Sci. USA 103: 383-388.
  • Chu, Z., M. Yuan, J. Yao, X. Ge, B. Yuan, C. Xu, X. Li, B. Fu, Z. Li, J.L. Bennetzen, Q. Zhang and S. Wang. 2006. Promoter mutations of an essential gene for pollen development result in disease resistance in rice. Genes Dev. 20: 1250-1255.
  • Bruggmann, R., A.K. Bharti, H. Gundlach, J. Lai, S. Young, A.C. Pontaroli, F. Wei, G. Haberer, G. Fuks, C. Du, C. Raymond, M.C. Estep, R. Liu, J. L. Bennetzen, A. P. Chan, P. D. Rabinowicz, J. Quackenbush7, W.B. Barbazuk, R.A. Wing, B. Birren, C. Nusbaum, S. Rounsley, K.F.X. Mayer, and J. Messing. 2006. Uneven chromosome contraction and expansion in the maize genome. Genome Res. 16: 1241-1251.
  • Vitte, C. and J.L. Bennetzen. 2006. Analysis of retrotransposon diversity uncovers properties and propensities in angiosperm genome evolution. Proc. Natl. Acad. Sci. USA 103: 17638-17643.
  • Chan, P.A., G. Pertea, F. Cheung, D. Lee, L. Zheng, A.C. Pontaroli, P. SanMiguel, Y. Yuan, J. Bennetzen, B. Barbazuk, J. Quackenbush, and P.D. Rabinowicz. 2006. The TIGR maize database. Nucl. Acids Res. 34: D771-D776.
  • Rabinowicz, P.D. and J.L. Bennetzen. 2006. The maize genome as a model for efficient sequence analysis of large plant genomes. Curr. Opin. Plant Biol. 9: 149-156.
  • Emberton J., Ma J.X., Yuan Y.N., SanMiguel P., and J. L. Bennetzen. 2005. Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Res. 15: 1441-1446.
  • Ma J.X., SanMiguel P., Lai J.S., Messing J., and J.L. Bennetzen. 2005. DNA rearrangement in orthologous Orp regions of the maize, rice and sorghum genomes. Genetics 170: 1209-1220.
  • Swigonova, Z., J.L. Bennetzen and J. Messing. 2005. Structure and evolution of the r/b chromosomal regions in rice, maize, and sorghum. Genetics 169: 891-906.
  • Bennetzen, J.L., J. Ma and K.M. Devos. 2005. Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 95: 127-132.
  • Muthukumar, B. and J.L. Bennetzen. 2004. Isolation and characterization of genomic and transcribed retrotransposon sequences from sorghum. Mol. Genet. Genomics 271: 308-316.
  • Ma, J., K.M. Devos and J.L. Bennetzen. 2004. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14: 860-869.
  • Yan, L., A. Loukoianov, A. Blechl, G. Tranquilli, W. Ramakishna, P. SanMiguel, J.L. Bennetzen, V. Echenique and J. Dubcovsky. 2004. The wheat Vrn2 gene is a flowering repressor downregulated by vernalization. Science 303: 1640-1644.
  • Ma, J. and J.L. Bennetzen. 2004. Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. USA 101: 12404-12410.
  • Kellogg, E.A. and J.L. Bennetzen. 2004. The evolution and phylogenetic relevance of nuclear genome structure in plants. Amer. J. Bot. 91: 1709-1725.
  • Swigonova, Z., J. Lai, J. Ma, W. Ramakrishna, V. Llaca, J.L. Bennetzen and J. Messing. 2004. Close split of sorgham and maize genome progenitors. Genome Res 14: 1916-1923.
  • Lai, J., J. Ma, Z. Swigonova, W. Ramakrishna, E. Linton, V. Llaca, B. Tanyolac, Y. Park, O. Jeong, J.L. Bennetzen, and J. Messing. 2004. Gene loss and movement in the maize genome. Genome Res. 14: 1924-1931.
  • Bennetzen, J.L., C. Coleman, R. Liu, J. Ma, and W. Ramakrishna. 2004. Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7: 732-736.
  • Gill B.S., Appels R., Botha-Oberholster A.M., Buell C.R., Bennetzen J.L., Chalhoub B., Chumley F., Dvorak J., Iwanaga M., Keller B., Li W., McCombie W.R., Ogihara Y., Quetier F. and T. Sasaki. 2004. A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics 168: 1087-96.
  • Yuan, Y., P. J. SanMiguel and J.L. Bennetzen. 2003. High Cot sequence analysis of the maize genome. Plant J., 34: 249-255.
  • Sanz-Alferez , S., P. SanMiguel , Y.-K. Jin, P. S. Springer and J.L. Bennetzen. 2003. Structure and evolution of the Cinful retrotransposon family of maize. Genome 46: 745-752.
  • Ilic, K., P. J. SanMiguel and J.L. Bennetzen. 2003. A complex history of rearrangement in an orthologous region of the maize, sorghum and rice genomes. Proc. Natl. Acad. Sci. USA 100: 12265-12270.
  • Whitelaw, C.A., Barbazuk, W.B., Pertea, G., Chan, A.P., Cheung, F., Lee, Y., Zheng, L., van Heeringen, S., Karamycheva, S., Bennetzen, J.L., SanMiguel, P., Lakey, N., Bedell, J., Yuan,Y.; Budiman, M.A., Resnick, A., Van Aken, S., Utterback, T., Riedmuller, S., Williams, M., Feldblyum, T., Schubert, K., Beachy,R., Fraser, C.M. and J. Quackenbush. 2003. Enrichment of gene-coding sequences in maize by genome filtration. Science 302: 2118-2120.
  • Bennetzen, J.L. 2003. Higher throughput comparative genomics of wheat and related cereals. Proceedings of the Tenth International Wheat Genetics Symposium 1: 215-220.
  • Bennetzen, J.L., and J. Ma. 2003. The genetic colinearity of rice and other cereals based on genomic sequence analysis. Curr . Opin . Plant Biol. 6: 128-133.
  • Ramakrishna, W. and J.L. Bennetzen. 2003. Genomic colinearity as a tool for plant gene isolation. Methods Mol. Biol. 236: 109-122.
  • “Characterization of the wheat genome by random BAC and sample sequencing,” NSF
  • "DOE Bioenergy Science Center," DOE
  • "Resource Development in Switchgrass, an Important Bioenergy Crop for the USA," USDA
  • “Cloning and Characterization of the Pc toxin resistance gene of Sorghum bicolor,” USDA
  • Maize Transposable Elements: Discovery, Description, and Functional Characterization," NSF
  • "Assessing the Reproductive Investments and Strategies Among Widely Disjunct Populations of Fringed Campion (Silene polypetala)," Georgia Department of Natural Resources