Back to Home

Sequencing the Maize Genome

Zea mays or maize is the highest-yielding crop worldwide and PGIR has also been involved in the maize genome projects. Several of those have been funded to prepare the sequencing of the genome, which at the time was difficult because of its size being larger than the human genome. The maize/sorghum collinearity project (PI, J. Messing, Rutgers University) sought to analyze the whole-genome duplication event that led to the formation of today’s maize genome. Because this project involved the sequencing of maize homoeologous regions, it also funded the construction of a BAC library (MboI) from the inbred B73. The Maize Mapping Project (MMP, PI, E. Coe Jr., University of Missouri) generated a genetic map from a recombinant inbred population derived from intermated B73 x Mo17 (IBM). It also included the construction of BAC libraries from inbred B73 (HindIII + EcoRI). BAC libraries from both sources consist of 458,905 clones covering the B73 genome of 2,365 Mb 29 times. In addition, the MMP sought to generate a physical map by DNA fingerprinting of the BAC libraries and linking them to the IBM map.

To further prepare for sequencing the entire genome, two additional projects were funded. The Sequencing the Maize Genome Project (STMG, PI, J. Messing, Rutgers University) sought to improve on the B73 physical map by High Information Content Fingerprinting (HICF) and by BAC end sequencing (BES). BESs serve as sequence tagged connectors (STCs) between sequences and the genetic map. They also represent a random comprehensive survey of genes and repeat elements of the maize genome. The third component of STMG was BAC sequencing from 100 random regions and to investigate assembly of shotgun reads, gene structure, and members of repetitive sequences. The second project, Consortium for Maize Genomics (CMG, PI, K. Schubert, Donald Danforth Plant Science Center), tested fractionation techniques of genomic regions containing only genes and not repetitive DNA elements. Both CMG and STMG have collaborated to sequence two homoeologous regions of the maize genome (7.8 Mb from Zm1S & 6.6 Mb from Zm9L, respectively) and to analyze maize genome structure and shotgun sequence assemblies of a larger interval. Based on a minimum tiling path generated from the maize map, the genome has been sequenced by the Washington University Genome Sequencing Center in collaboration with Arizona Genome Institute and Cold Spring Harbor Laboratory.

In addition to laying the foundation for the maize genome sequence, we also participated in a maize genome project focused on genes expressed in the endosperm of the maize seed with a consortium involving the laboratories
of Don McCarty, Curt Hannah, Mark Settles, Karen Koch at the University of Florida at Gainesville, Phil Becraft at Iowa State University, and Brian Larkins at the University of Arizona, Tucson. This project also known as the uniformMu project used the transposable element mutator as a mutagen for gene-knockouts. We generated full-length cDNAs from endosperm of the same genetic background, inbred W22. We sequenced those and junction sequences of mutator insertions in the genome. Out of 23,348 high-quality cDNA sequence reads, we obtained 5,326 unigenes, reflecting the endosperm transcriptome. All the above projects have been National Science Foundation sponsored projects and ended in 2008.

More recently, we received institutional support to use the maize genome data for evolutionary studies.
Additional information can be found on the Maize Genetics and Genomics Database.


  • Song, R., Llaca, V., Linton, E., and Messing, J. (2001). Sequence, regulation, and evolution of the maize 22-kDa  zein gene family.  Genome Research 11, 1817-1825.
  • Ramakrishna, W., Ma, J., SanMiguel, P., Emberton, J., Dubcovsky, J., Shiloff, B. A., Jiang, Z., Rostocks, N., Busso, C. S., Ogden, M., Linton, E., Kleinhofs, A., Devos, K. M., Messing, J., Bennetzen, J. (2002). Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis. Comp. Funct. Genom. 3, 165-166.
  • Song, R., Llaca, V., and Messing, J. (2002). Mosaic organization of orthologous sequences in grass genomes. Genome Research 12, 1549-1555.
  • Song, R. and Messing, J. (2002). Contiguous genomic DNA sequence comprising the 19-kDa-zein gene family from Zea mays. Plant Physiol. 130, 1626-1635.
  • Ramakrishna, W., Emberton, J., SanMiguel, P., Ogden, M., Llaca, V., Messing, J., and Bennetzen, J.L. (2002). Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex. Plant Physiol. 130, 1728-1738.
  • Yim, Y-S., Davis, G., Duru, N., Musket, T., Linton, E. W., Messing, J. W., McMullen, M. D., Soderlund, C., Polacco, M., Gardiner, J. and Coe Jr., E. H. (2002). Characterization of three maize BAC libraries toward anchoring of the physical map to the genetic map using high density BAC filter hybridization. Plant Physiol. 130, 1686-1696.
  • Song, R. and Messing, J. (2003). Gene expression of a gene family in maize based on non-collinear haplotypes. Proc. Natl. Acad. Sci. USA 100, 9055-9060.
  • Lai, J., Dey, N., Kim, C-S., Bharti, A.K., Rudd, S., Mayer, K.F.X, Larkins, B.A., Becraft, P., and Messing J. 2004. Characterization of the maize endosperm transcriptome and its comparison to the rice genome. Genome Res. 14, 1932-1937.
  • Messing, J., Bharti, A.K., Karlowski, W.M., Gundlach, H., Kim, H.-R., Yu, Y., Wei, F., Fuks, G., Soderlund, C.A., Mayer, K.F.X., and Wing, R.D. (2004). Sequence Composition and Genome Organization of Maize. Proc. Natl. Acad. Sci. USA. 101, 14349-14354.
  • Clark, RM, Linton, E, Messing, J, and Doebley, JF (2004). "Pattern of diversity in the genomic region near the domestication gene tb1." Proc Natl Acad Sci USA 101, 700-707.
  • Swigoňová, Z., Lai, J., Ma, J., Ramakrishna, W., Llaca, V., Bennetzen, J.L., and Messing, J. 2004. On the tetraploid origin of the maize genome. Comp. Funct. Genomics 5, 281-284.
  • Swigoňová, Z., Lai, J., Ma, J., Ramakrishna, W., Llaca, V., Bennetzen, J.L., and Messing, J. 2004. Close split of maize and sorghum genome progenitors. Genome Res. 14, 1916-1923.
  • Lai, J., Ma, J., Swigoňová, Z., Ramakrishna, W., Linton, E., Llaca, V., Tanyolac, B. Park, Y-J., Jeong, O-Y., Bennetzen, J.L., and Messing, J. 2004. Gene loss and movement in the maize genome. Genome Res. 14, 1924-1931.
  • Swigoňová, Z., Bennetzen, J.L., and Messing, J. 2005. Structure and evolution of the r/b chromosomal regions in rice, maize, and sorghum. Genetics, 169, 891-906.
  • Lai, J., Li, Y., Messing, J., and Dooner, H. (2005). Gene movement by Helitrons contributes to the haplotype variability of maize. Proc. Natl. Acad. Sci. USA. 102, 968-973.
  • Ma, J., SanMiguel, P., Lai, J., Messing, J., and Bennetzen,  J.L. (2005). DNA Rearrangement in Orthologous Orp Regions of the Maize, Rice and Sorghum Genomes. Genetics 170, 1209-1230.
  • Nelson, W.M., Bharti, A.K., Butler, E., Wei, F. Fuks, G., Kim, H-R., Wing, R.A., Messing, J. and Soderlund, C. (2005). Whole-Genome Validation of High-Information-Content Fingerprinting. Plant Phys. 139, 27-38.
  • McCarty, D.R., Settles, A., Suzuki, M., Tan, B-C., Latshaw, S., Porch, T., Robin, K., Baier, J., Avigne, W., Lai, J., Messing, J., Koch, K., and Hannah, L.C. (2005). Steady-state transposon mutagenesis in inbred maize. Plant J. 44, 52-61.
  • Haberer, G., Young, S., Bharti, A.K., Gundlach, H., Raymond, C., Fuks, G., Butler, E., Wing, R.A., Rounsley, S., Birren, B., Nusbaum, C., Mayer, K.F.X, and Messing, J. (2005). Structure and Architecture of the Maize Genome. Plant Phys. 139, 1612-1624.
  • Messing J. (2005). The maize genome. Maydica 50, 377-386.
  • Messing, J. and Dooner, H. (2006). Organization and variability of the maize genome. Curr. Opin. Plant Biol. 9, 157-63.
  • Bruggmann, R. Bharti, A.K., Gundlach, H. Lai, J., Young, S., Pontaroli, A.C., Wei, F., Haberer, G., Fuks, G., Du, C. Raymond, C., Estep, M.C., Liu, R., Bennetzen, J.L., Chan, A., Rabinowicz, P.D., Quackenbush, J., Barbazuk, W.B., Wing, R.A., Birren, B., Nusbaum, C., Rounsley, S., Mayer, K.F.X, and Messing, J. (2006). Uneven Chromosome Contraction and Expansion in the Maize Genome. Genome Research 16, 1241-1251.
  • Du, C., Swigonova, Z., and Messing, J. (2006). Retrotranspositions in orthologous regions of closely related grass species. BMC Evol. Biol. 6, e62.
  • Xu, J. and Messing, J. (2006). Maize haplotype with a helitron-amplified cytidine deaminase gene copy. BMC Genetics 7, e52.
  • Nelson, W.M., Dvorak, J., Luo, M-C., Messing, J., Wing, R.A., Soderlund, C. (2007) Efficacy of clone fingerprinting methodologies. Genomics 89, 160-165.
  • Settles, A.M., Holding, D.R., Tan, B.C., Latshaw, S.P., Liu, J., Suzuki, M., Li, L., O'Brien, B.A., Fajardo, D.S., Wroclawska, E., Tseung, C.W., Lai, J., Hunter, C.T. 3rd, Avigne, W.T., Baier, J., Messing, J., Hannah, L.C., Koch, K.E., Becraft, P.W., Larkins, B.A., McCarty, D.R. (2007) Sequence-indexed mutations in maize using the UniformMu transposon-tagging population. BMC Genomics 8, e116.
  • Wei, F., Coe, E., Nelson, W., Bharti, A.K., Engler, F., Butler, E., Kim, H., Goicoechea, J.L., Chen, M., Lee, S., Fuks, G., Sanchez-Villeda, H., Schroeder, S., Fang, Z., McMullen, M., Davis, G., Bowers, J.E., Paterson, A.H., Schaeffer, M., Gardiner, J., Cone, K., Messing, J., Soderlund, C., and Wing, R.A. (2007) Physical and Genetic Structure of the Maize Genome Reflects its Complex Evolutionary History. PLoS Genetics 3, 3123.
  • Messing, J. and Bennetzen, J. (2008). Grass Genome Structure and Evolution. In: Genome Dynamics, ed. Volff, J.-N., vol. 4, Karger Basel, Switzerland, pp. 41-56.
  • Xu, J. and Messing, J. (2008). Diverged copies of the seed regulatory Opaque-2 geneby a segmental duplication in the progenitor genome of rice, sorghum, and maize. Mol. Plant 1, 760-769.
  • Xu, J. and Messing, J. (2008). Organization of the prolamin gene family provides insight into the evolution of the maize genome and gene duplications in grass species. Proc. Natl. Acad. Sci. USA 105, 14330-14335.
  • Nelson, W., Luo, M., Ma, J., Estep, M., Estill, J., He, R., Talag, J., Sisneros, N., Kudrna, D., Kim, H., Ammiraju, J.S., Collura, K., Bharti, A.K., Messing, J., Wing, R.A., Sanmiguel, P., Bennetzen, J.L., and Soderlund, C. (2008) Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains. BMC Genomics 19, e621.
  • Messing, J. (2009). The Structure of the Maize Genome. In: Molecular Genetic Approaches to Maize Improvement, Biotechnology in Agriculture and Forestry, Vol. 63, eds. Kriz, A. L. & Larkins, B. A., Springer Verlag, New York, NY, pp. 213-230.
  • Messing, J. (2009). The Polyploid Origin of Maize. In: The Maize Handbook: Domestication, Genetics, and Genome, eds. Bennetzen, J. L. & Hake, S. C., Springer Verlag, New York, NY, pp. 221-238.
  • Bolot, S., Abrouk, M., Masood-Quraishi, U., Stein, N., Messing, J., Feuillet, C., Salse, J. (2009) The 'inner circle' of the cereal genomes. Curr. Opin. Plant Biol., Epubl. ahead of print.
  • Goettel, W. and Messing, J. (2009). Change of gene structure and function by non-homologous end-joining, homologous recombination, and transposition of DNA. PLoS Genet. 5, e1000516.
  • Salse, J., Abrouk, M., Bolot, S., Guilhot, N., Courcelle, E., Faraut, T., Waugh, R., Close, T.J., Messing, J., and Feuillet, C. 2009. Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc. Natl. Acad. Sci. USA 106, 14908-14913.
  • Xu, J-H. and Messing, J. (2009). Amplification of Prolamin Storage Protein Genes in different subfamilies of the Poaceae. Theor Appl Genet 119, 1397-1412.
  • Abrouk, M., Murat, F., Pont, C., Messing, J., Jackson, S., Faraut, T., Tannier, E., Plomion, C., Cooke, R., Feuillet, C., and Salse, J. (2010) Palaeogenomics Q1 of plants: synteny based modelling of extinct ancestors. Trends in Plant Sci. 15, 479-487.
  • Murat, F., Xu, J-H., Tannier, E., Abrouk, M., Pont, C. Messing, J., and Salse, J. (2010). Mechanisms Driving Dynamic Chromosome Evolutionary Plasticity as a Source of Novel Plant Species. Genome Res. 11, 1545-1557.
  • Goettel, W. and Messing, J. (2010). Divergence of gene regulation through chromosomal rearrangements. BMC Genomics 11, e678.
  • Amundsen, K., Rotter, D., Jung, G., Messing, J., Belanger, F. and Warnke, S. (2011). Miniature Inverted-Repeat Transposable Element Identification and Genetic Marker Development in Agrostis. Crop Science 51, 854-861.
  • Xu, J.-H., Bennetzen, J.L., and Messing, J. (2012) Dynamic Gene Copy Number Variation in Collinear Regions of Grass Genomes. Mol. Biol. & Evolution 29, 861-871.