Jeffrey Bennetzen


Contact Information:


Phone: 706-542-9235
E-mail: maize@uga.edu
Address:
Department of Genetics
C424 Life Sciences Building
Athens, GA 30602

Education:


  • Ph.D. in Biochemistry at the University of Washington (1980).
  • B.A. in Biology at the University of California, San Diego (1974).

Research and Teaching Positions:


  • Graduate Student, Departments of Biochemistry and Genetics, University of Washington (1974-1980).
  • Postdoctoral Fellow, Washington University, Stanford University, and University of California, Berkeley (1980-1981).
  • Research Scientist, Plant Pathology Group, International Plant Research Institute, San Carlos, California (1981-1983).
  • Assistant Professor, Department of Biological Sciences, Purdue University, West Lafayette, Indiana (1983-1987).
  • Associate Professor, Department of Biological Sciences, Purdue University, West Lafayette, Indiana (1987-1991).
  • Visiting Scholar, Sainsbury Laboratory, John Innes Centre, Norwich, England (1990-1991).
  • Professor, Department of Biological Sciences, Purdue University, West Lafayette, Indiana (1991-2003).
  • Co-Director, Purdue Genetics Program (1997-1999).
  • Visiting Professor, Section of Plant Biology, University of California at Davis (1998).
  • H. Edwin Umbarger Distinguished Professor of Genetics (1999-2003).
  • Norman and Doris Giles Eminent Scholar Chair in Molecular Biology and Functional Genomics, Department of Genetics, University of Georgia, Athens, Georgia (2003-present).
  • Adjunct Professor, Department of Plant Biology, University of Georgia (2004-present).
  • Faculty Member, Institute of Bioinformatics, University of Georgia (2004-present).
  • First Réseaux Thématiques de Recherche Avancée (RTRA) Senior Fellow, CIRAD, Montpellier, France (2008).
  • Head, Department of Genetics, University of Georgia, Athens, Georgia (2009-2011).

Awards:


  • Guggenheim Fellowship, 2008 .
  • RTRA (France) Senior Fellowship, first recipient, 2008.
  • Elected Fellow, American Association for the Advancement of Science, 2005.
  • Elected to US National Academy of Sciences, 2004.
  • Georgia Research Alliance Endowed Professorship in Genetics, 2003.
  • Pandit Jawaharlal Nehru Centenary Professorship, University of Hyderabad, 2002.
  • Umbarger Endowed Professorship in Genetics, 1999.
  • Sigma Xi Faculty Research Award, 1995.
  • Fulbright Awards, 1990 and 2008.
  • Presidential Young Investigator Award, National Science Foundation, 1986.
  • McKnight Foundation Award in Plant Biology, 1986.
  • B.A., Biology, with Highest Honors, University of California, San Diego, 1974.

Research Interests:


  • Plant genome structure and evolution, especially the nature of rearrangements and the contributions of transposable elements.
  • The relationship between genome structure/evolution and gene function.
  • Genetic diversity in crop plants and their wild relatives.
  • The rapid evolution of complex disease resistance loci in plants.
  • Fine structure recombinational analysis.
  • The coevolution of plant/microbe and plant/parasite interactions, primarily in the soil.
  • The genetic basis of lignocellulosic biomass quality and quantity in grasses.
  • The breeding and genetic engineering of plants with improved resistances to abiotic and/or biotic stresses by the use of major resistance genes.

Referred Research Publications (145):


  • Williamson, V. M., J. Bennetzen, E. T. Young, K. Nasmyth and B. D. Hall (1980) Isolation of the structural gene for alcohol dehydrogenase by genetic complementation in yeast. Nature 283:214-216.
  • Lescure, B., J. Bennetzen and A. Sentenac (1981) In vitro transcription of the yeast alcohol dehydrogenase I gene by homologous RNA polymerase B.  (II) Selective initiation and discontinuous elongation on a supercoiled template. J. Biol. Chem. 256:1018-1024.
  • Nagamine, Y., J. Bennetzen, A. Sentenac and P. Fromageot (1981) Single-stranded DNA transcription by yeast RNA polymerase B. Biochim. Biophys. Acta 656:220-227.
  • Bennetzen, J. L. and B. D. Hall (1982) The primary structure of the Saccharomyces cerevisiae gene for alcohol dehydrogenase I.  J. Biol. Chem. 257:3018-3025.
  • Bennetzen, J. L. and B. D. Hall (1982) Codon selection in yeast.  J. Biol. Chem. 257:3026-3031.
    Strommer, J. N., S. Hake, J. Bennetzen, W. C. Taylor and M. Freeling (1982) Regulatory mutants of the Adh1 gene in maize caused by DNA insertions. Nature 300:542-544.
  • Dennis, E. S., W. L. Gerlach, A. J. Pryor, J. L. Bennetzen, A. Inglis, D. Llewellyn, M. Sachs, R. J. Ferl and W. J. Peacock (1984) The Adh1 gene of maize. Nucl. Acids Res. 12:3983-4000.
  • Bennetzen, J. L., J. Swanson, W. C. Taylor and M. Freeling (1984) An insertion in the first intron of maize Adh1 affects transcript levels:  Cloning of progenitor and mutant alleles. Proc. Natl. Acad. Sci. USA 81:4125-4128.
  • Barker, R. F., D. V. Thompson, D. R. Talbot, J. Swanson and J. L. Bennetzen (1984) Nucleotide sequence of the maize transposable element Mu1.  Nucl. Acids Res. 12:5955-5967.
  • Bennetzen, J. L. (1984) Transposable element Mu1 is found in multiple copies only in Robertson's Mutator maize lines. J. Mol. Appl. Genet. 2:519-524.
  • Bennetzen, J. L. and T. L. Adams (1984) Selection and characterization of cadmium-resistant suspension cultures of the wild tomato Lycopersicon peruvianum. Plant Cell Rep. 3:258-261.
  • Bennetzen, J. L. (1987) Covalent DNA modification and the regulation of Mutator element transposition in maize. Mol. Gen. Genet. 208:45-51.
  • Bennetzen, J. L., R. P. Fracasso, D. W. Morris, D. S. Robertson and M. J. Skogen-Hagenson (1987) Concomitant regulation of Mu1 transposition and Mutator activity in maize. Mol. Gen. Genet. 208:57-62.
  • Lee, L., C. Fenoll and J. L. Bennetzen (1987) Construction and homologous expression of a maize Adh1 based NcoI cassette vector. Plant Physiol. 85:327-330.
  • Bennetzen, J. L., M.-M. Qin, S. Ingels and A. H. Ellingboe (1988) Allele-specific and Mutator-associated instability at the Rp1 disease resistance locus of maize. Nature 332:369-370.
  • Bennetzen, J. L., W. E. Blevins and A. H. Ellingboe (1988) Cell-autonomous recognition of the rust pathogen determines Rp1-specified resistance in maize. Science 241:208-210.
  • Brown, W. E., D. S. Robertson and J. L. Bennetzen (1989) Molecular analysis of multiple Mutator-derived mutations at the Bronze locus in maize. Genetics 122:439-445.
  • Eckdahl, T. T., J. L. Bennetzen and J. N. Anderson (1989) DNA structures associated with autonomously replicating sequences from plants. Plant Mol. Biol. 12:507-516.
  • Jin, Y.-K. and J. L. Bennetzen (1989) Structure and coding properties of the maize retrotransposon Bs1. Proc. Natl. Acad. Sci. USA 86:6235-6239.
  • Springer, P. S., E. A. Zimmer and J. L. Bennetzen (1989) Genomic organization of the ribosomal DNA of sorghum and its close relatives. Theor. Appl. Genet. 77:844-850.
  • Hulbert, S. H., T. E. Richter, J. D. Axtell and J. L. Bennetzen (1990) Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. Proc. Natl. Acad. Sci. USA 87:4251-4255.
  • Hulbert, S. H. and J. L. Bennetzen (1991) Recombination at the Rp1 locus of maize. Mol. Gen. Genet. 226:377-382.
  • Hulbert, S. H., P. C. Lyons and J. L. Bennetzen (1991) Reactions in maize lines carrying Rp resistance genes to isolates of the common rust pathogen, Puccinia sorghi. Plant Disease 75:1130-1133.
  • Lyznik, L. A., J. D. McGee, P.-Y. Tung, J. L. Bennetzen and T. K. Hodges (1991) Homologous recombination between plasmid DNA molecules in maize protoplasts. Mol. Gen. Genet. 230:209-218.
  • Ingels, S. C., J. L. Bennetzen, S. H. Hulbert, M.-M. Qin and A. H. Ellingboe (1992) Mutator transposable elements that occur in clusters in the maize genome. J. Hered. 83:114-118.
  • Sudupak, M. A., J. L. Bennetzen and S. H. Hulbert  (1992) Unequal exchange and meiotic instability of Rp1 region disease resistance genes in maize. Genetics 133:119-125.
  • Hong, K. S., T. E. Richter, J. L. Bennetzen and S. H. Hulbert (1993) Complex duplications in maize lines. Mol. Gen. Genet. 239:115-121.
  • Melake-Berhan, A., S. H. Hulbert, L. G. Butler and J. L. Bennetzen  (1993) Structure and evolution of the genomes of Sorghum bicolor and Zea mays. Theor. Appl. Genet. 86:598-604.
  • Avramova, Z. and J. L. Bennetzen  (1993) Isolation of matrices from maize leaf nuclei and identification of a matrix-binding site adjacent to the Adh1 gene. Plant Mol. Biol. 22:1135-1143.
  • Simcox, K. D. and J. L. Bennetzen  (1993) The use of molecular markers to study Setosphaeria turcica resistance in maize. Phytopath. 83:1326-1330.
  • Zanta, C. A., X. Yang, J. D. Axtell and J. L. Bennetzen  (1994) The candystripe locus, y-cs, determines mutable pigmentation of the sorghum leaf, flower, and pericarp. J. Hered. 85:23-29.
  • Springer, P. S., K. J. Edwards and J. L. Bennetzen (1994) DNA class organization on maize Adh1 yeast artificial chromosomes. Proc. Natl. Acad. Sci. U.S.A. 91:863-867.
  • Bennetzen, J. L. and P. S. Springer  (1994) The generation of Mutator transposable element subfamilies in maize. Theor. Appl. Genet. 87:657-667.
  • Thomas, C. M., D. A. Jones, J. J. English, B. J. Carroll, J. L. Bennetzen, K. Harrison, A. Burbidge, G. J. Bishop and J. D. G. Jones (1994) Analysis of the chromosomal distribution of transposon-carrying T-DNAs in tomato using the inverse polymerase chain reaction. Mol. Gen. Genet. 242:573-585.
  • Jin, Y.-K. and J. L. Bennetzen (1994) Integration and nonrandom mutation of a plasma membrane proton ATPase gene fragment within the Bs1 retroelement of maize.  Plant Cell 6:1177-1186.
  • Brown, W. E., P. S. Springer and J. L. Bennetzen (1994) Progressive modification of Mu transposable elements during development. Maydica 39:119-126.
  • Bennetzen, J. L., K. Schrick, P. S. Springer, W. E. Brown and P. SanMiguel (1994) Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 37:565-576.
  • Bennetzen, J. L. (1994) Inactivation and reactivation of mutability at a Mutator-derived bronze1 allele in maize. Maydica 39:309-317.
  • Cresse, A. D., S. H. Hulbert, W. E. Brown, J. R. Lucas and J. L. Bennetzen (1995) Mu1-related transposable elements of maize preferentially insert into low copy number DNA. Genetics 140:315-324.
  • Sanz-Alferez, S., T. E. Richter, S. H. Hulbert and J. L. Bennetzen (1995) The Rp3 disease resistance gene of maize: mapping and characterization of introgressed alleles. Theor. Appl. Genet. 91:25-32.
  • Richter, T. E., A. J. Pryor, J. L. Bennetzen and S. H. Hulbert (1995) New rust resistance specificities associated with recombination in the Rp1 complex in maize. Genetics 141:373-381.
  • Salimath, S. S., A. C. de Oliveira, I. D. Godwin and J. L. Bennetzen (1995). Assessment of genome origins in the genus Eleusine with DNA markers. Genome 38:757-763.
  • Avramova, Z., P. SanMiguel, E. Georgieva and J. L. Bennetzen (1995) Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1. Plant Cell 7:1667-1680.
  • Kantety, R. V., X. Zeng, J. L. Bennetzen and B. E. Zehr (1995) Assessment of genetic diversity in dent and popcorn (Zea mays L.) inbred lines using inter-simple sequence repeat (ISSR) amplification. Molecular Breeding 1:365-373.
  • Oliveira, A. C., T. Richter and J. L. Bennetzen (1996) Regional and racial specificities in sorghum germplasm assessed with DNA markers. Genome 39:579-587.
  • Buckner, B., P. SanMiguel, D. Janick-Buckner and J. L. Bennetzen (1996) The Y1 gene of maize codes for phytoene synthase. Genetics 143:479-488.
  • Edwards, K. J., J. Veuskens, H. Rawles, A. Daly and J. L. Bennetzen (1996) Characterization of four dispersed repetitive DNA sequences in Zea mays and their use in constructing contiguous DNA fragments using YAC clones. Genome 39: 811-817.
  • SanMiguel, P., A. Tikhonov, Y.-K. Jin, N. Motchoulskaia, D. Zakharov, A. Melake-Berhan, P. S. Springer, K. J. Edwards, M. Lee, Z. Avramova and J. L. Bennetzen (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765-768.
  • Yang, W., A. C. Oliveira, I. D. Godwin, K. Schertz and J. L. Bennetzen (1996) Comparison of DNA marker technologies in characterizing plant genome diversity: variability in Chinese sorghums. Crop Sci. 36:1669-1676.
  • Avramova, Z., A. Tikhonov, P. SanMiguel, Y.-K. Jin, C. Liu, S.-S. Woo, R. A. Wing and J. L. Bennetzen (1996) Gene identification in a complex chromosomal continuum by local genomic cross-referencing. Plant J. 10:1163-1168.
  • Chen, M. and J. L. Bennetzen (1996) Sequence organization in the Sh2/A1-homologous region of rice. Plant Mol. Biol. 32:999-1001.
  • Chen, M., P. SanMiguel, A. C. de Oliveira, S.-S. Woo, H. Zhang, R. A. Wing and J. L. Bennetzen (1997) Microcolinearity in the sh2-homologous regions of the maize, rice and sorghum genomes. Proc. Natl. Acad. Sci. USA  94:3431-3435.
  • Frederick, R. D., J. Chiu, J. L. Bennetzen and A. K. Handa (1997) Identification of a pathogenicity locus, rpfA, in Erwinia caratovora subsp. carotovora that encodes a two component sensor/regulator protein. Mol. Plant Microbe Interact. 10:407-415.
  • Chen, M., P. SanMiguel and J. L. Bennetzen (1998) Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148:435-443.
  • Avramova, Z., A. Tikhonov, M. Chen and J. L. Bennetzen (1998) Matrix-attachment regions and structural colinearity in the genomes of two grass species. Nucl. Acids Res. 26:761-767.
  • Bennetzen, J. L., P. SanMiguel, M. Chen, A. Tikhonov, M. Francki and Z. Avramova (1998) Grass genomes. Proc. Natl. Acad. Sci. USA 95:1975-1978.
  • SanMiguel, P. and J. L. Bennetzen (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Annals Bot. 82:37-44.
  • SanMiguel, P., B. S. Gaut, A. Tikhonov, Y. Nakajima and J. L. Bennetzen (1998) The paleontology of intergene retrotransposons of maize. Nature Genet 20:43-45.
  • Tikhonov, A. P., P. J. SanMiguel, Y. Nakajima, N. D. Gorenstein, J. L. Bennetzen and Z. Avramova (1999) Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc. Natl. Acad. Sci. USA 96:7409-7414.
  • Tikhonov, A. P., J. L. Bennetzen and Z. Avramova (2000) Structural domains and matrix attachment regions along colinear chromosomal segments of maize and sorghum. Plant Cell 12:249-264.
  • Tikhonov, A.P., L. Lavie, C. Tatout, J. L. Bennetzen, Z. Avramova and J. M. Deragon (2001) Target sites for SINE integration in Brassica genomes display nuclear matrix binding activity. Chrom. Res. 9:325-337.
  • Dubcovsky, J., W. Ramakrishna, P. SanMiguel, C. S. Busso, L. Yan, B. A. Shiloff and J. L. Bennetzen (2001) Comparative sequence analysis of colinear barley and rice BACs. Plant Physiol. 125:1342-1353.
  • Xu, J. C., Y. M. Weerasuriya and J. L. Bennetzen (2001) Construction of genetic map in sorghum and fine mapping of the germination stimulant production gene response to Striga asiatica. Acta Genetica Sinica (in chinese) 28:870-876 (published w/o knowledge of JLB).
  • Reddy, A. R., W. Ramakrishna, A. C. Sekhar, N. Ithal, P. R. Babu, M. F. Bonaldo, M. B. Soares and J. L. Bennetzen (2002) Novel genes are enriched in normalized cDNA libraries from drought stressed seedlings of indica rice (Oryza sativa L. cv. Nagina 22). Genome 45:204-211.
  • SanMiguel, P.J., W. Ramakrishna, J. L. Bennetzen, C. S. Busso and J. Dubcovsky (2002) Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5Am. Functional and Integrative Genomics 2:51-59.
  • Rostoks, N., Y.-J. Park, W. Ramakrishna, J. Ma, A. Druka, B. A. Shiloff, P. J. SanMiguel, Z. Jiang, R. Brueggeman, D. Sandhu, K. Gill, J. L. Bennetzen and  A. Kleinhofs (2002) Genomic sequencing reveals gene content, genomic organization and  recombination relationships in barley. Functional and Integrative Genomics 2:70-80.
  • Ghebru, B., Schmidt, R. J. and J. L. Bennetzen (2002) Genetic diversity of Eritrean sorghum landraces assessed with Simple Sequence Repeat (SSR) markers. Theor. Appl. Genet. 105:229-236.
  • Devos, K. M., J. K. M. Brown and J. L. Bennetzen (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12:1075-1079.
  • Yuan, Y., P. J. SanMiguel and J. L. Bennetzen (2002) Methylation-spanning linker libraries link gene-rich regions and identify epigenetic boundaries in Zea mays. Genome Res. 12:1345-1349.
  • Ramakrishna, W., J. Emberton, M. Ogden, P. SanMiguel and J. L. Bennetzen (2002) Sequence and physical map analyses of the maize Rp1 complex uncovers numerous sites and unexpected mechanisms of local rearrangement. Plant Cell 14:3213-3223.
  • Yan, L., V. Echenique, C. Busso, W. Ramakrishna, P. SanMiguel, J. L. Bennetzen, S. Harrington and J. Dubcovsky (2002) Cereal genes from the SNF2 family are members of a new subfamily that includes human and mouse genes. Mol. Genetics and Genomics 268:488-499.
  • Stam, M., C. Belele, W. Ramakrishna, J. Dorweiler, J. L. Bennetzen and V. L. Chandler (2002) The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162:917-930.
  • Ramakrishna, W., J. Dubcovsky, Y.-J. Park, C. Busso, J. Emberton, P. SanMiguel and J. L. Bennetzen (2002) Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162:1389-1400.
  • Ramakrishna, W., J. Emberton, P. SanMiguel, M. Ogden, V. Llaca, J. Messing and J. L. Bennetzen (2002) Comparative sequence analysis of the sorghum rph region and the maize rp1 resistance gene complex. Plant Physiol. 130:1728-1738.
  • Yuan, Y., P. J. SanMiguel and J. L. Bennetzen (2003) High Cot sequence analysis of the maize genome. Plant J., 34:249-255.
  • 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.
  • 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 46:747-752.
  • Whitelaw C. A., W. B. Barbazuk, G. Pertea, A. P. Chan, F. Cheung, Y. Lee, L. Zheng, S. van Heeringen, S. Karamychev1, J. L. Bennetzen, P. SanMiguel, N. Lakey, J. Bedell, Y. Yuan, M. A. Budiman, A. Resnick, S. Van Aken, T. Utterback, S. Riedmuller,  M. Williams, T. Feldblyum, K. Schubert, R. Beachy, C. M. Fraser and J. Quackenbush (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302:2118-2120.
  • Muthukumar, B. and J. L. Bennetzen (2004) Isolation and characterization of genomic and transcribed retrotransposon sequences from sorghum. Mol. Genet. Genomics 271:308-316.
  • 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., 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.
  • Ma, J. and J. L. Bennetzen (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. USA 101:12404-12410.
  • Swigonova, Z., J. Lai, J. Ma, W. Ramakrishna, V. Llaca, J. L. Bennetzen and J. Messing (2004) Close split of sorghum and maize genome progenitors. Genome Res. 14:1916-1923.
  • Lai, J., J. Ma, Z. Swigonova, W. Ramakrishna, E. Linton, V. Llaca, B. Tanyolac, Y.-J. Park, O.-Y. Jeong, J. L. Bennetzen and J. Messing (2004) Gene loss and movement in the maize genome. Genome Res. 14:1924-1931.
  • Bennetzen, J. L., J. Ma and K. M. Devos (2005) Mechanisms of recent genome size variation in flowering plants. Annals Bot. 95:127-132.
  • 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.
  • Ma, J., J. Lai, J. Messing and J. L. Bennetzen (2005) DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes. Genetics 170:1209-1220.
  • Emberton, J., J. Ma, Y. Yuan and J. L. Bennetzen (2005) Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Res. 15:1441-1446.
  • Devos, K. M., J. Ma, A. C. Pontaroli, L. H. Pratt and J. L. Bennetzen (2005) Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. Proc. Natl. Acad. Sci. USA 102:19243-19248.
  • 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. Quackenbush, 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.
  • 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.
  • Nagy, E., T.-C. Lee, W. Ramakrishna, Z. Xu, P. E. Klein, P. San Miguel, 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 to 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.
  • Dida, M. M., S. Srinivasachary, S. Ramakrishnan, J. L. Bennetzen, M. D. Gale and K. M. Devos (2007) The genetic map of finger millet, Eleusine coracana. Theor. Appl. Genet. 114:321-332.
  • 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.
  • Rensing, S. A., D. Lang, A. Zimmer, A. Terry, A. Salamov, H. Shapiro, T. Nishiyama, P.-F. Perroud, E. Lindquist,Y. Kamisugi, T. Tanahashi, K. Sakakibara, T. Fujita, K. Oishi, T. Shin, Y. Kuroki, A. Toyoda, Y. Suzuki, S. Hashimoto, K. Yamaguchi, S. Sugano, Y. Kohara, A. Fujiyama, A. Anterola, S. Aoki, N. Ashton, W. B. Barbazuk, E. Barker, J. L. Bennetzen, R. Blankenship, S. H. Cho, S. Dutcher, M. Estelle, J. A. Fawcett, H. Gundlach, K. Hanada, A. Heyl, K. A. Hicks, J. Hughes, M. Lohr, K. Mayer, A. Melkozernov, T. Murata, D. Nelson, B. Pils, M. Prigge, B. Reiss, T. Renner, S. Rombauts, P. Rushton, A. Sanderfoot, G. Schween, S.-H. Shiu, K. Stueber, F. L. Theodoulou, H. Tu, Y. Van de Peer, P. J. Verrier, E. Waters, A. Wood, L. Yang, D. Cove, A. C. Cuming, M. Hasebe, S. Lucas, B. D. Mishler, R. Reski, I. Grigoriev, R. S. Quatrano and J. L. Boore (2008) The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants. Science 319:64-69.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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 9:621.
  • 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 20:3191-3209.
  • Baucom, R. S., J. C. Estill, J. Leebens-Mack and J. L. Bennetzen (2009) Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 19:243-254.
  • Lu, F., J. S. S. Ammiraju, A. Sanyal, S. Zhang, R. Song, J. Chen, G. Li, Y. Sui, Z. Cheng, A. C. de Oliveira, J. L. Bennetzen, S. A. Jackson, R. A. Wing and M. Chen (2009) Comparative sequence analysis of MONOCULM1-orthologous regions in fourteen Oryza genomes. Proc. Natl. Acad. Sci. USA 106:2071-2076.
  • Pontaroli, A. C., R. L. Rogers, Q. Zhang, M. E. Shields, T. M. Davis, K. M. Folta, P. SanMiguel and J. L. Bennetzen (2009) Gene content and distribution in the nuclear genome of Fragaria vesca. Plant Genome 2:83-91.
  • Estill, J. C. and J. L. Bennetzen (2009) The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes. Plant Methods 5:8 (online).
  • Yang, L. and J. L. Bennetzen (2009) Structure-based discovery and description of plant and animal Helitrons. Proc. Natl. Acad. Sci. USA 106:12832-12837.
  • Yang, L. and J. L. Bennetzen (2009) Distribution, diversity, evolution and survival of Helitrons in the maize genome. Proc. Natl. Acad. Sci. USA 106:19922-19927.
  • Tian, Z., C. Rizzon, J. Du, B. S. Gaut, J. L. Bennetzen, S. A. Jackson and J. Ma (2009) Genetic recombination shapes the pattern of DNA acquisition and elimination mediated by LTR-retrotransposons in rice. Genome Res. 19:2221-2230.
  • Schnable., P. et al.: Maize Genome Sequencing Consortium [~160 authors; R. Baucom, J. Estill, L. Yang, J. L. Bennetzen included] (2009) The B73 maize genome: complexity, diversity and dynamics. Science 326:1112-1115.
  • Baucom, R. S., J. C. Estill, N. Upshaw, A. Jogi, C. Chapparro, J. M. Deragon, R. R. Westerman, P. J. SanMiguel, and J. L. Bennetzen (2009) Exceptional diversity, non-random distribution and rapid evolution of retroelements in the B73 maize genome. PLOS Genetics 5: e1000732. doi:10.1371/journal.pgen.1000732.
  • Wei, F., J. C. Stein, C. Liang, J. Zhang, R. S. Fulton, R. S. Baucom, E. de Paoli, S. Zhou, L. Yang, Y. Han, S. Paternak, A. Narechania, L. Zhang, C.-T. Yeh, K. Ying, D. H. Nagel, K. Collura, D. Kudrna, J. Currie, J. Lin, H. Kim, A. Angelove, G. Scara, M. Wissotski, W. Golser, L. Courtney, S. Kruchowski, T. Graves, S. Rock, S. Adams, L. Fulton, C. Fronick, W. Courtney, M. Kramer, L. Spiegel, L. Nascimento, A. Kalyanaraman, C. Chaparro, J.-M. Deragon, P. SanMiguel, N. Jiang, S. R. Wessler, P. J. Green, Y. Yu, D. C. Schwartz, B. C. Meyers, J. L. Bennetzen, R. Martienssen, W. R. McCombie, S. Aluru, S. W. Clifton, P. S. Schnable, D. Ware, R. K. Wilson and R. A. Wing (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLOS Genetics 5: e1000728. doi:10.1371/journal.pgen.1000728.
  • Davis, T. M., M. E. Shields, Q. Zhang, D. C. Tombolato, J. L. Bennetzen, A. C. Pontaroli, H. Wang, Q. Yao, P. SanMiguel and K. M. Folta. (2010) An examination of targeted gene neighborhoods in strawberry. BMC Plant Biol. 10:81, publ. online.
  • Jetty, S., C. Fan, Y. Yu, X. Song, K. Cranston, A. C. Pontaroli, F. Lu, A. Sanyal, N. Jiang, T. Rambo, J. Currie, K. Collura, J. Talag, J. L. Bennetzen, M. Chen, S. Jackson and R. A. Wing (2010) Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. Plant J. 63:430-442.
  • Shulaev, V. et al. [66 authors, including H. Wang and J. L. Bennetzen] (2011) The genome of woodland strawberry (Fragaria vesca).  Nature Genetics 43:109-116.
  • Banks, J. A. et al. [103 authors, including J. DeBarry, L. Feng, L. Yang, Q. Zhu and J. L. Bennetzen)] (2011) The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants. Science 332:960-963.
  • Al-Dous, E. K., B. George, M. E. Al-Mahmoud, M. Y. Al-Jaber, H. Wang, Y. M. Salameh, E. K. Al-Azwani, S. Chaluvadi, A. C. Pontaroli, J. DeBarry, J. Ohlrogge, V. Arondel, I. J. Saie, K. M. Suliman-Elmeer, J. L. Bennetzen, R. R. Kruegger and J. A. Malek (2011) De novo genome sequencing and comparative genomics of the date palm (Phoenix dactylifera). Nature Biotech. 29:521-527.
  • Mann, D. G. J., Z. R. King, W. Liu, B. L. Joyce, R. J. Percifield, J. S. Hawkins, P. R. LaFayette, B. J. Artelt, J. N. Burris, M. Mazarei, J. L. Bennetzen, W. A. Parrott, and C. N. Stewart, Jr. (2011) Switchgrass (Panicum virgatum L.) ubiquitin gene (PvUbi1 and PvUbi2) promoters for use in plant transformation.  BMC Biotech. 11:74 (doi: 10.1186/1472-6750-11-74).
  • Estep, M., T. A. Van Mourik, P. Muth, D. Guindo, H. K. Parzies, O. A. Koita, E. Weltzien, and J. L. Bennetzen (2011) Genetic diversity of a parasitic weed, Striga hermonthica, on sorghum and pearl millet in Mali. Tropical Plant Biol. 4:91-98.
  • Xu, J.-H., J. L. Bennetzen and J. Messing (2012) Dynamic gene copy number variation in collinear regions of grass genomes.  Mol. Biol. Evol. 29:861-871.
  • Bennetzen, J. L., J. Schmutz, H. Wang, R. Percifield, J. Hawkins, A. C. Pontaroli, M. Estep, L. Feng, J. N. Vaughn, J. Grimwood, J. Jenkins, K. Barry, E. Lindquist, U. Hellsten, S. Deshpande, X. Wang, X. Wu, T. Mitros, J. Triplett, X. Yang, C.-Y. Ye, M. Mauro-Herrera, L. Wang, P. Li, M. Sharma, R. Sharma, P. C. Ronald, O. Panaud, E. A. Kellogg, T. Brutnell, A. Doust, G. A. Tuskan, D. Rokhsar and K. M. Devos (2012) Full genome sequence analysis of the model plant Setaria.  Nature Biotech. 30:555-561.
  • Smith, S. M., Y. Yuan, A. N. Doust and J. L. Bennetzen (2012) Haplotype analysis and linkage disequilibrium at five loci in Eragrostis tef. G3: Genes, Genomes, Genetics 2:407-419.
  • Estep, M. C., B. S. Gowda, K. Huang, M. P. Timko and J. L. Bennetzen (2012) Genomic characterization for parasitic weeds of the genus Striga by sample sequence analysis. Plant Genome 5:30-41.
  • Urano, D., J. C. Jones, H. Wang, M. Mathew, W. Bradford, J. L. Bennetzen and A. M. Jones (2012) G protein activation without a GEF in the plant kingdom. PLoS Genetics, online (doi:10.1371/journal.pgen.1002756).
  • Wu, J., Z. Wang, Z. Shi, S. Zhang, R. Ming, S. Zhu, M. Awais Khan, S. Tao, S. S. Korbans, H. Wang, N. J. Chen, T. Nishio, X. Xu, L. Cong, K. Qi, X. Huang, Y. Wang, X. Zhao, J. Wu, C. Deng, C. Gou, W. Zhou, H. Yin, G. Qin, Y. Sha, Y. Tao, H. Chen, Y. Yang, Y. Song, D. Zhan, J. Wang, L. Li, M. Dai, C. Gu, Y. Wang, D. Shi, X. Wang, H. Yang, L. Zeng, C. Zheng, C. Wang, M. Chen, G. Wang, L. Xie, V. Sovero, S. Sha, W. Huang, S. Zhang, M. Zhang, J. Sun, L. Xu, Y. Li, X. Liu, Q. Li, J. Shen, J. Wang, R. E. Paull, J. L. Bennetzen, J. Wang and S. Zhang (2012) The genome of pear (Pyrus bretschneideri Rehd). Genome Res. 23:396-408.
  • Zhu, Q., S. M. Smith, M. Ayele, L. Yang, A. Jogi, S. Chaluvadi and J. L. Bennetzen (2012) High throughput discovery of mutations in tef semi-dwarfing genes by next generation sequence analysis. Genetics 192:819-829.
  • Wang, H. and J. L. Bennetzen (2012) Centromere retention and loss during the descent of maize from a tetraploid ancestor.  Proc. Natl. Acad. Sci. USA 109:21004-21009.
  • Estep, M. C., J. D. DeBarry and J. L. Bennetzen (2013) The dynamics of LTR retrotransposon accumulation across 35 million years of panicoid grass evolution.  Heredity 110:194-204.
  • Parvathaneni, R. K., V. Jakkula, F. K. Padi, S. Faure, N. Nethra, A. C. Pontaroli, X. Wu, J. L. Bennetzen, and K. M. Devos (2013) Fine mapping and identification of a candidate gene underlying the d2 dwarfing phenotype in pearl millet, Cenchrus americanus (L.) Morrone. G3: Genes, Genomes and Genetics 3:567-572.
  • Wu, J. [and 59 other authors, including H. Wang and J. L. Bennetzen] (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 23:396-408.
  • Zhu, Q., J. L. Bennetzen and S. M. Smith (2013) Isolation and diversity analysis of resistance gene homologues from switchgrass. G3: Genes, Genomes and Genetics 3:1031-1042.
  • Vitte, C., M. Estep, J. Leebens-Mack and J. L. Bennetzen (2013) Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes. Annals Bot. 112:881-889.
  • Chao, M., H. Wang, D. Chung, J. L. Bennetzen and J. Westpheling (2013) Isolation and bioinformatics analysis of a novel transposable element, ISCbe4, from the hyperthermophilic bacterium, Caldicellulosiruptor besciiJ. Industrial Micro. Biotech., 40:1443-1448.
  • Wang, C., X. Shi, L. Liu, H. Li, J. S. S. Ammiraju, D. A. Kudrna, W. Xiong, H. Wang, Z. Dai, Y. Zheng, J. Lai, W. Jin, J. Messing, J. L. Bennetzen, R. A. Wing and M. Luo (2013) Genomic resources for gene discovery, functional genome annotation and evolutionary studies of maize and its close relatives. Genetics 195:723-727.
  • Vaughn, J. N. and J. L. Bennetzen (2014) Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair. Proc. Natl. Acad. Sci. USA 111:6684-6689.
  • Chaluvadi, S. R., S. Khanam, M. Aly and J. L. Bennetzen (2014) Diversity and population structure of native and introduced date palm (Phoenix dactylifera) germplasm in the United Arab Emirates. Trop. Plant Biol 7:30-41.
  • Hawkins, J. S., V. Delgado, L. Feng, M. Carlisle, H. K. Dooner and J. L. Bennetzen (2014) Variation in allelic expression associated with a recombination hotspot in Zea mays. Plant. J., 79:375-384.
  • Vaughn, J. N., S. R. Chaluvadi, Tushar, L. Rangan and J. L. Bennetzen (2014) Whole plastome sequences from five ginger species facilitate marker development and define limits to barcode methodology. PLoS ONE 9: e108581. doi: 10.1371/journal.pone.0108581.
  • Zhang, Q.-J., T. Zhu, E.-H. Xia, C. Shi, Y.-L. Liu, Y. Zhang, Y. Liu, W.-K. Jiang, Y.-J. Zhao, S.-Y. Mao, L.-P. Zhang, H. Huang, J.-Y. Jiao, P.-Z. Xu, Q.-Y. Yao, F.-C. Zeng, L.-L. Yang, J. Gao, D.-Y. Tao, Y.-J. Wang, J. L. Bennetzen and L.-Z. Gao (2014) Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1418307111.
  • Wang, H., K. M. Devos and J. L. Bennetzen (2014) Recurrent loss of specific introns during angiosperm evolution. PLoS Genetics, in press.

Reviews, Commentaries, Perspectives and Related Articles
(some referred, some not) (51):


  • Bennetzen, J. L. and S. H. Hulbert (1992) Organization, instability, and evolution of plant disease resistance genes.  Plant Mol. Biol. 20:575-578.
  • Bennetzen, J. L., P. A. Springer, A. D. Cresse and M. Hendrickx (1993) Regulation and specificity of the Mutator transposable element system in maize.  In B. V. Conger, ed., Critical Reviews in Plant Sciences 12:57-95.
  • Bennetzen, J. L. and M. Freeling  (1993) Grasses as a single genetic system:  genome composition, collinearity and complementarity.  Trends Genet. 9:259-261.
  • Bennetzen, J. L. (1995) Biotechnology for sorghum improvement.  African Crop Sci. J. 3:161-170.
  • Bennetzen, J. L. (1996) The contributions of retroelements to plant genome organization, function and evolution. Trends Micro 4:347-353.
  • Bennetzen, J. L. and M. Freeling (1997) The unified grass genome: synergy in synteny. Genome Res. 7:301-307.
  • Bennetzen, J. L. and E. A. Kellogg (1997) Do plants have a one way ticket to genomic obesity? Plant Cell 9:1509-1514.
  • Bennetzen, J. L., E. A. Kellogg, M. Lee and J. Messing (1998) A plant genome initiative. Plant Cell 10:488-493.
  • Bennetzen, J. L. (1998) The structure and evolution of angiosperm nuclear genomes. Curr. Opin. Plant Biol. 1:103-108.
  • Bennetzen, J. L. (1999) Plant genomics takes root, branches out. Trends Genet. 15:85-87.
  • Kumar, A. and J. L. Bennetzen (1999) Plant retrotransposons. Ann. Rev. Genet. 33:479-532.
  • Bennetzen, J. L. (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42:251-269.
  • Bennetzen, J. L. (2000) The many hues of plant heterochromatin. Genome Biol.  1:107.1-107.4.
  • Bennetzen, J. L. (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12:1021-1029.
  • Kumar, A. and J. L. Bennetzen (2000) Retrotransposons: central players in the structure, evolution and function of plant genomes. Trends Plant Sci. 5:509-510.
  • Bennetzen, J., E. Buckler, V. Chandler, J. Doebley, J. Dorweiler, B. Gaut, M. Freeling, S. Hake, E. Kellogg, R. S. Poethig, V. Walbot and S. Wessler (2001) Genetic evidence and the origin of maize. Latin American Antiquity 12:84-86.
  • Bennetzen, J. L. (2001) Arabidopsis arrives. Nature Genet. 27:3-5.
  • Bennetzen, J. L., V. L. Chandler and P. Schnable (2001) National Science Foundation-sponsored workshop report. Maize genome sequencing project. Plant Physiol. 127:1572-1578.
  • Bennetzen, J. L. and K. M. Devos (2002) Plant synteny, colinearity and genome evolution. Encycl. Life Sci., http://www.els.net. London: Nature Publishing Group.
  • Bennetzen, J. L. (2002) Functional genomics in plants. Encyl. Life Sci., http://www.els.net. London: Nature Publishing Group.
  • Bennetzen, J. L. and W. Ramakrishna (2002) Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol. Biol., 48:821-827.
  • Bennetzen, J. L. (2002) Opening the door to comparative plant biology. Science 296:60-63.
  • Bennetzen, J. L. (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115:29-36.
  • Bennetzen, J. L. and W. Ramakrishna (2002) Exceptional haplotype variation in maize. Proc. Natl. Acad. Sci. USA 99:9093-9095.
  • 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.
  • 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., C. Coleman, J. Ma, R. Liu and W. Ramakrishna (2004) Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7:732-736.
  • 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.
  • Gill, B. S., R. Appels, A.-M. Botha-Oberholster, C. R. Buell, J. L. Bennetzen, B. Chalhoub, F. Chumley, J. Dvoák, M. Iwanaga, B. Keller, W. Li, W. R. McCombie, Y. Ogihara, F. Quetier and T. Sasaki (2004) A workshop report on wheat genome sequencing. Genetics 168:1087-1096.
  • Bennetzen, J. L. (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr. Opin. Gen. Dev. 15:1-7.
  • Bennetzen, J. L., R. Liu, J. Ma and A. Pontaroli (2005) Maize genome structure and rearrangement. Maydica (50th anniversary issue) 50:387-392.
  • 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.
  • 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.
  • Bennetzen, J. L. (2007) Patterns in grass genome evolution. Curr. Opin. Plant Biol. 10:176-181.
  • 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.
  • 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 (2008) A unified classification system for eukaryotic transposable elements implemented in Repbase. Nature Rev. Genet. 9:414.
  • Liu, R. and J. L. Bennetzen (2008) Enchilada redux:  How complete is your genome sequence? New Phytol. 179:249-250.
  • Bennetzen, J. L. and M. Chen (2008) Grass genomic synteny illuminates plant genome function and evolution. RICE 1:109-118.
  • Doust, A. N., E. A. Kellogg, K. M. Devos and J. L. Bennetzen (2009) Foxtail millet (Setaria italica): a sequence-driven grass model system. Plant Physiol. 149:137-141.
  • Bennetzen, J. L. (2009) Biology and the beasts: individual investigator-driven research in the megaprojects era. Trends Genet. 25:57-59 (Inaugural article, Science and Society section).
  • Gleick, P. H. and 254 additional U. S. National Academy of Sciences members (incl. J. L. Bennetzen) (2010) Climate change and the integrity of science. Science 328:689-690.
  • Molecular Ecology Resources Primer Development Consortium [136 authors, including J. L. Bennetzen and M. Estep] (2010) Permanent genetic resources added to Molecular Ecology Resources database 1 April 2010 – 31 May 2010. Molec. Ecol. Res. 10:1098–1105.
  • Lisch, D., and J. L. Bennetzen (2011) Transposable element origins of epigenetic gene regulation. Curr. Opin. Plant Biol. 14:156-161.
  • Zhu, J.-K. and J. L. Bennetzen (2011) Epigenetics of the epigenome.  Curr. Opin. Plant Biol. 14:113-115.
  • Galbraith, D. W., J. L. Bennetzen, E. A. Kellogg, J. C. Pires and P. S. Soltis (2011) The genomes of all angiosperms: a call for a coordinated global census. J. Bot., online (doi:10.1155/2011/646198).
  • Khanam, S., A. Sham, J. L. Bennetzen and M. A. M. Aly (2012) Analysis of molecular marker-based characterization and genetic variation in date palm (Phoenix dactylifera L.). Australian J. Crop Sci. 6:1236-1244.
  • Kuester, A., B. Foltz, G. Lor, S. Chang, J. Bennetzen, and R. Baucom (2013) Development and characterization of simple sequence repeat loci for the common morning glory, Ipomoea purpurea (Convolvulaceae). Mol. Ecol. Resources 13:341-343.
  • Bennetzen, J. L., and H. Wang (2014) The contributions of transposable elements to the structure, function and evolution of plant genomes.  Ann. Rev. Plant Biol. 65:505-530.
  • Diao, X., J. Schnable, J. L. Bennetzen and J. Li (2014) Initiation of Setaria as a model plant. Front. Agr. Sci. Eng. 1:16-20.

Books:


  • Bennetzen, J. L., and S. C. Hake (2009) The Maize Handbook - Volume I: It's Biology. Springer, New York, pp. 1-587.
  • Bennetzen, J. L., and S. Hake (2009) The Maize Handbook - Volume II: Genetics and Genomics. Springer, New York, pp. 1-798.

Book Chapters:


  • Bennetzen, J. L. (1984) Genetic engineering for improved crop disease resistance.  In G. B. Collins and J. F. Petolino, eds., Applications of Genetic Engineering to Crop Improvement.  Martinus Nijhof/Dr. W. Junk, Dordrecht, Netherlands, pp. 491-524.
  • Bennetzen, J. L. (1985) The regulation of Mutator function and Mu1 transposition.  UCLA Symp. Mol. Cell. Biol. 35:343-354.
  • Handa, A. K., R. A. Bressan, L. Lee, D. J. Charles, R. K. Jayaswal, J. Chiu and J. L. Bennetzen (1987) Characterization of pathogenicity genes of Erwinia carotovora.  In D. P. S. Verma and N. Brisson, eds., Molecular Genetics of Plant-Microbe Interactions. Martinus Nijhof, Dordrecht, Netherlands, p. 67-72.
  • Bennetzen, J. L., A. Cresse, W. E. Brown and L. Lee (1987) Molecular cloning of maize genes by transposon tagging with Mutator.  UCLA Symp. Mol. Cell. Biol., 62:183-204.
  • Bennetzen, J. L., W. E. Brown and P. S. Springer (1988) DNA modification within and flanking maize transposable elements.  In O. E. Nelson, Jr., ed., Plant Transposable Elements.  Plenum Press, New York, pp. 237-250.
  • Bennetzen, J. L., S. H. Hulbert, P. J. San Miguel, C. Carter-Peek, J. Chiu and A. K. Handa (1988) Microbial interactions with maize.  In D. P. Verma and R. Palacios, eds., Molecular Genetics of Plant-Microbe Interactions, 1988.  APS Press, St. Paul, pp. 268-270.
  • Handa, A. K., J. Chiu, H. Rozycki and J. L. Bennetzen (1989) Evidence for global regulation of the expression of pathogenicity genes in soft rot Erwinias.  Proceedings of the 7th Int'l. Conf. on Plant Path. Bacteria, Hungarian Acad. Sci., Budapest, 707-712.
  • Bennetzen, J. L., S. H. Hulbert and P. C. Lyons (1991) Fine structure analysis of a maize disease resistance gene.  In S. S. Patil, D. Mills and C. Vance, eds., Molecular Strategies of Pathogens and Host Plants.  Springer Verlag, New York, pp. 177-188.
  • Bennetzen, J. L. and J. D. G. Jones (1992) Approaches and progress in the molecular cloning of plant disease resistance genes.  In J. K. Setlow, ed., Genetic Engineering, Principles and Methods, Vol. 14.  Plenum Press, New York, pp. 99-124.
  • Bennetzen, J. L., S. Sanz-Alferez, K. S. Hong, T. E. Richter, R. D. Frederick, P. SanMiguel and S. H. Hulbert (1994) Molecular genetic analysis of rust resistance genes in maize.  In A. Bianchi, E. Luppotto and M. Motto, eds., Eucarpia, Breeding and Molecular Biology: Accomplishments and Future Promises.  Bergamo, pp. 258-264.
  • Bennetzen, J. L. and A. Melake-Berhan (1994) Generation of a genetic map for Sorghum bicolor.  In R. L. Phillips and I. K. Vasil, eds., DNA-Based Markers in Plants.  Kluwer, Dordrecht, pp. 291-298.
  • Brown, W. E. and J. L. Bennetzen (1994) Transposon tagging technologies in maize.  In Y. T. S. Bajaj, ed., Biotechnology in Agriculture and Forestry:  Biotechnology in Maize Issue.  Springer Verlag, New York, pp. 385-401.
  • Bennetzen, J. L., T. Richter, G. Hu, P. SanMiguel, K. Hong, R. Frederick and S. Hulbert  (1994)  Organization and hyperevolution of rust resistance genes in maize.  In M. J. Daniels, J. A. Downie and A. E. Osbourn, eds., Advances in the Molecular Genetics of Plant-Microbe Interactions.  Kluwer, Dordrecht, pp. 261-266.
  • Bennetzen, J. L., P. SanMiguel, C.-N. Liu, M. Chen, A. Tikhonov, A. C. Oliveira, Y.-K. Jin, Z. Avramova, S.-S. Woo, H. Zhang and R. A. Wing (1996) Microcollinearity and segmental duplication in the evolution of grass nuclear genomes. In: J.S. Heslop-Harrison, ed., Unifying Plant Genomes, Company of Biologists, Ltd., Cambridge, pp. 1-3.
  • Bennetzen, J. L. (1996) The Mutator transposable element system of maize.  In H. Saedler and A. Gierl, eds., Transposable Elements, Springer-Verlag, Berlin, pp. 195-229.
  • Bennetzen, J. L. (1996) The use of comparative genome mapping in the identification, cloning and manipulation of important plant genes.  In B. W. S. Sobral, ed., The Impact of Plant Molecular Genetics. Birkhauser, Boston, pp. 71-86.
  • Bennetzen, J. L., C.-N. Liu, P. SanMiguel, P. S. Springer, Y.-K. Jin, C. A. Zanta and Z. Avramova (1996) Commonalites and contrasts in the organization of the maize and sorghum nuclear genomes. In J. P. Gustafson and R. B. Flavell, eds., Genomes of Plants and Animals, Plenum, New York, pp. 103-114.
  • Bennetzen, J. L. (1998) The potential of biotechnology for the improvement of sorghum and pearl millet. Proc. 1996 Int'l Conf. on Genetic Improvement of Sorghum and Pearl Millet. INTSORMIL/ICRISAT Press, pp. 13-20.
  • Bennetzen, J. L. (1998) The evolution of grass genome organisation and function. In A. Greenland, E. M. Meyerowitz and M. Steer, eds., Control of Plant Development: Genes and Signals. Company of Biologists, Ltd., Cambridge, pp. 123-126.
  • Bennetzen, J. L. (1998) The grasses as a single genetic system. In I. K. Vasil, ed., Molecular Improvement of Cereal Crops. Kluwer Academic, Dordrecht, pp. 387-394.
  • Bennetzen, J.L., F. Gong, J. Xu, C. Newton and A. C. de Oliveira (2000) The study and engineering of resistance to the parasitic weed striga in rice, sorghum and maize.  In B. I. G. Haussmann, D. E. Hess, M. L. Koyama, L. Grivet, H. F. W. Rattunde and H. H. Geiger, eds., Breeding for Striga Resistance in Cereals. Margraf Verlag, Weikersheim, Germany, pp. 197-206.
  • Bennetzen, J. L., V. Subramanian, J. Xu, S. S. Salimath, S. Subramanian, D. Bhattramakki and G. E. Hart (2001) A framework genetic map of sorghum containing RFLP, SSR and morphological markers. In R. L. Phillips and I. K. Vasil, eds., DNA-Based Markers in Plants (2nd Ed.). Kluwer Academic, Dordrecht, pp. 347-356.
  • Paterson, A. H. and J. L. Bennetzen (2001) Comparative mapping of plant chromosomes. In R. L. Phillips and I. K. Vasil, eds., DNA-Based Markers in Plants (2nd Ed.). Kluwer Academic, Dordrecht, pp. 101-114.
  • Devos, K. M. and J. L. Bennetzen (2001) Genome relationships: Maize and the grass model. In S. Brenner and J. H. Miller, eds., Encyclopedia of Genetics, Academic Press, New York, pp 863-865.
  • Bennetzen, J. L. (2001) Studies of genome structure and evolution in the cereals using comparative genomic sequencing. In KAST, eds., The Second Hallim International Symposium on Recent Advances in Life Science and Biotechnology, KAST Press, Seoul, Korea, pp. 27-47.
  • Bennetzen, J. L. and M. Ayele (2001) Genetic characterization of tef in the context of overall studies of grass genome content, organization, evolution and function. In H. Tefera, G. Belay and M. Sorrells, eds., Narrowing the Rift: Tef Research and Development, EARO Press, Addis Ababa, Ethiopia, pp. 121-130.
  • Bennetzen, J. L. (2003) Rapid genome change in maize and sorghum. In press.
  • Ramakrishna, W. and J. L. Bennetzen (2003) Genomic colinearity as a tool for plant gene isolation. In E. Grotewold, ed., Plant Functional Genomics. Humana Press, Totowa, NJ, pp 109-122.
  • Bennetzen, J. L. (2005) Modes, rates and mechanisms of local genomic change in flowering plants: tempest in a pea plot. In F. T. Bakker, L. W. Chatrou, B. Gravendeel and P. B. Pelser, eds., Plant Species-level Systematics: new perspectives on pattern & process. Koeltz Scientific Books, Koenigstein, Germany, pp. 305-316.
  • Messing, J. and J. L. Bennetzen (2008) Grass genome structure and evolution.  In J.-N. Volff, ed., Genome Dynamics Vol. 4: Plant Genomes. Karger Publ., Basel, Switzerland, pp. 41-65.
  • Devos, K. M., A. Costa de Oliveira, X. Xu, J. Estill, M. Estep, A. Jogi, M. Morales, J. Pinheiro, P. SanMiguel and J. L. Bennetzen (2008) Structure and organization of the wheat genome – the number of genes in the hexaploid wheat genome. In: R. Appels, R. Eastwood, E. Lagudah, P. Langridge, M. Mackay, L. McIntyre, and P. Sharp, eds., Proc. 11th International Wheat Genet. Symp. Sydney University Press, Sydney, pp. 1-5.
  • Bennetzen, J. L. (2009) Maize genome structure and evolution. In J. L. Bennetzen and S. Hake, eds., The Maize Handbook – Volume II: Genetics and Genomics. Springer, New York, pp. 179-200.
  • Bennetzen, J. L. (2009) The future of maize. In J. L. Bennetzen and S. Hake, eds., The Maize Handbook - Volume II: Genetics and Genomics. Springer, New York, pp. 771-780.
  • Bennetzen, J. L., S. M. Smith, Y. Yuan and D. Groth (2009) Comparative plant biology: Opening new avenues for the improvement of orphan crops in a time of rapid and potentially catastrophic change in worldwide agriculture. In: Z. Tadele, ed., New Approaches to Plant Breeding of Orphan Crops in Africa: Proceedings of an International Conference. Univ. Bern, Stampfli AG, Bern, pp. 11-20.
  • Wusirika, R., K. Li, R. L. Phillips and J. L. Bennetzen (2011) Zea. In: C. Kole, ed., Wild Crop Relatives: Genomic and Breeding Resources. Vol 1: Wild Relatives of Cereals. Springer Verlag, Berlin, Heidelberg, pp. 457-488.
  • Deshpande, A., A. C. Pontaroli, S. R. Chaluvadi, F. Lu, and J. L. Bennetzen (2011) Plant genetics for study of the roles of root exudates and microbes in soil.  In: A. Costa de Oliveira and R. K. Varshney, eds., Root Genomics, Springer, pp. 99-112.
  • Vitte, C., T. Peterson and J. L. Bennetzen (2011) Transposable elements and the evolving structure of the maize genome.  In: J. L. Prioul, ed., Advances in Maize, Taylor and Francis, Soc. Exp. Biol., London, pp. 2-36.
  • Fedoroff, N. V. and J. L. Bennetzen (2013) Transposons, genomic shock and genome evolution. In:  N. V. Fedoroff, ed., Plant Transposons and Genome Dynamics in Evolution, John Wiley & Sons, pp. 181-201.

Published Abstracts, Book Reviews, Letters and Newsletter Articles:


  • Zimmer, E., J. Swanson, C. Rivin, S. Hake, J. L. Bennetzen and V. Walbot (1981) Rapid evolution of ribosomal and other repeated DNAs in corn and its relatives.  Fed. Proc. 40:1752.
  • Freeling, M., W. C.  Taylor and J. L. Bennetzen (1983) Mu1 transposable element.  Maize Genet. Coop. Newsl.  57:12-13.
  • Freeling, M., J. N. Strommer, S. Hake, M. S. Johns, M. Alleman, W. C. Taylor, J. L. Bennetzen and J. Swanson (1983) Consequences of insertion in the Adh1 gene of maize. J. Cell Biochem.  7B:260.
  • Strommer, J. N., J. L. Bennetzen, M. Alleman and M. Freeling (1983) Robertson’s Mutator transposable elements of maize.  J. Cell. Biochem. 7B:283.
  • Bennetzen, J. L. (1984) The molecular genetics of transposable elements in plants.  DNA  3:53.
  • Bennetzen, J. L. (1985) The mechanism, rate, regulation, and specificity of Mu1 transposition in maize.  J. Cell. Biochem.  9C:211.
  • Bennetzen, J. L., A. D. Cresse, W. E. Brown, R. P. Fracasso, C. Carter-Peek and D. Horvath (1987) Transposon tagging of maize regulatory and resistance genes using Mutator.  J. Cell. Biochem. 11B:16.
  • Bennetzen, J. L., C. Lin, S. McCormick and B. J. Staskawicz (1988) Transformation of Adh null pollen to Adh+  by macroinjection.  Maize Genetics Coop. Newsl.  62:113-114.
  • Brown, W. E., P. S. Springer, A. D. Cresse, D. S. Robertson and J. L. Bennetzen (1988) Developmental regulation of Mutator activity in maize.  J. Cell Biochem. 12C:190.  
  • Bennetzen, J. L. (1988) Somatic and germinal mutational analysis of the Rp1 disease resistance locus of maize.  J. Cell Biochem. 12C:244.
  • Bennetzen, J. L., P. J. San Miguel, R. A. Larson and R. W. Tuveson (1988) Structure and protective role of the carotenoid synthesis gene(s) of Erwinia Stewartii.  J. Cell Biochem. 12C:246.
  • Jin, Y.-K and J. L. Bennetzen (1988) Molecular characterization of a retroviral transposable element of maize.  J. Cell Biochem. 12C:296.
  • Bennetzen, J. L. and P. San Miguel (1989) The rescue of late field pollinations.  Maize Genetics Coop. Newsl. 63:126-128.
  • Bennetzen, J. L. (1989) A note on RFLP probes: their dissemination and utilization.  Maize Genetics Coop. Newsl. 63:128.
  • Bennetzen, J. L., S. H. Hulbert, A. Melake-Berhan and T. E. Richter (1991) Molecular analysis of the sorghum genome.  Sorghum Newsl.  32:6.
  • Springer, P. S. and J. L. Bennetzen (1992) Placement of teosinte branched on the linkage map.  Maize Genetics Coop. Newsl.  66:116.
  • Buckner, B., P. San Miguel and J. L. Bennetzen (1993) The Y1 gene codes for phytoene synthase.  Maize Genetics Coop. Newsl.  67:65.
  • Simcox, K. D. and J. L. Bennetzen (1993) Mapping the HtN resistance gene to the long arm of chromosome 8.  Maize Genetics Coop. Newsl.  67:118-119.
  • Bennetzen, J. L. (1994) Harvest for the world? (Book review of Genes, Crops and Environment by J. Holden, W. J. Peacock and T. Williams) Trends Genet. 10:32.
  • Kantety, R. V., X. Zeng, J. L. Bennetzen and B. E. Zehr (1995) Detection of high levels of polymorphism among dent and popcorn inbred lines using Inter-Simple Sequence Repeat (ISSR) amplification technique. Maize Genetics Coop. Newsl. 69:132-134.
  • Oliveira, A. C. and J. Bennetzen (1995) Analysis of Mu element relatedness by TIR comparison. Maize Genetics Coop. Newsl. 69:134-135.
  • Yang, W., P. SanMiguel, P. Stinard, D. Robertson and J. Bennetzen (1995) Opaque mutations from Mutator self populations. Maize Genetics Coop. Newsl. 69:135-136.
  • Springer, P. S. and J. L. Bennetzen (1995) Tlr1 may be allelic to tb1. Maize Genetics Coop. Newsl. 69:136.
  • Avramova, Z., E. Georgieva, A. Tikhonov and J.L. Bennetzen (1995) Chromatin domain organization around the maize adhl gene; mapping of MARs and potential transcriptional units along a continuous chromosomal region. J. Cell Biochem., Suppl. 21B: 128.
  • Bennetzen, J. L. and E. A. Kellogg (1998) Reply to “Slow but steady:  Reduction of genome size through biased mutation” letter from Dmitri Petrov.  Plant Cell 10:1901-1902.
  • Bennetzen, J. L. (2002) Assessment of gene content, colinearity and evolution in barley, maize, rice, sorghum and wheat. Maize Genetics Coop. Newsl. 76:93-94.
  • Messing, J., E. Linton, R. Song, J. Lai, B. Tanyolac, C. Kulikowski, I. Muchnik, A. Pereira do Lago, G. Fuks, G. Armhold, W. Ramakrishna, J. Ma, Y.-J. Park, J. Emberton, P. SanMiguel and J. L. Bennetzen (2002) Colinearity of maize and sorghum at the DNA sequence level. Maize Genetics Coop. Newsl. 76:83-86.
  • Ramakrishna W, J. X. Ma, P. SanMiguel, J. Emberton, J. Dubcovsky, B. A. Shiloff, Z. Y. Jiang, N. Rostoks, C. S. Busso, M. Ogden, E. Linton, A. Kleinhofs, K. M. Devos, J. Messing and J. L. Bennetzen (2002) Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis. Compar. Funct. Genomics 3:165-166.
  • Beachy, R., J. L. Bennetzen, B. M. Chassy, M. Chrispeels, J. Chory, J. R. Ecker, J. P. Noel, S. A. Kay, C. Dean, C. Lamb, J. Jones, C. R. Santerre, J. I. Schroeder, J. Umen, M. Yanofsky, S. Wessler, Y. Zhao and W. Parrott (2002) Divergent perspectives on GM food. Nature Biotech. 20:1195-1196.
  • Swigonova, Z., J. Lai, J. Ma, W. Ramakrishna, V. Llaca, J. L. Bennetzen, J. Messing (2004) On the tetraploid origin of the maize genome. Compar. Funct. Genom. 5:281-284.