Sequencing the Maize Genome

Zea mays or maize is the highest-yielding crop worldwide and its genome is the next plant genome to be sequenced. Several projects have already been funded to prepare for such an effort. The maize/sorghum collinearity project (PI, J. Messing, Rutgers University) sought to analyze the whole-genome duplication event that led to the formation of todayÕs 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), sought to test 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. All the above projects have been supported by the National Science Foundation.

Based on a minimum tiling path generated from the maize map, 17,000 BAC clones will be sequenced by the Washington University Genome Sequencing Center in collaboration with Arizona Genome Institute and Cold Spring Harbor Laboratory. In addition, random shotgun clones (fosmids) will be sequenced by the Washington University Genome Sequencing Center in collaboration with PGIR.

Click HERE for background, for STATUS of HICF and BES.
Results from these projects are presented on Websites sponsored by different collaborators:

PGIR: This Website is a portal for the STMG project; it also lists other maize genomics project and provides an ftp site for the download of trace and sequence files.

AGI/AGCoL: This Website sponsors the high-resolution physical map of maize inbred B73.

Broad Institute: This Website provides information on the BAC sequences.

MIPS: This Website provides the annotation of sequences produced by STMG.


Selected readings from the above projects:

*Bruggmann R, *Bharti AK, *Gundlach H, Lai J, Young SK, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC,
Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S,
Mayer KFX and Messing J (2006) Uneven chromosome contraction and expansion in the maize genome. Genome Res 16: 1241-1251.
(*Equal First Authors) Cover Page Article

*Haberer G, *Young SK, *Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Nusbaum C, Birren B,
Mayer KFX and Messing J (2005) Structure and architecture of the maize genome. Plant Physiol. 139: 1612-24.
(*Equal First Authors)

*Nelson WM, *Bharti AK, Butler E, Wei F, Fuks G, Kim HR, Wing RA, Messing J and Soderlund CA (2005) Whole-genome validation of
high-information-content fingerprinting. Plant Physiol 139: 27-38. (*Equal First Authors)

Cone KC, McMullen MD, Bi IV, Davis GL, Yim YS, Gardiner JM, Polacco ML, Sanchez-Villeda H, Fang Z, Schroeder SG,
Havermann SA, Bowers JE, Paterson AH, Soderlund CA, Engler FW, Wing RA and Coe EH Jr. (2002) Genetic, physical, and
informatics resources for maize. On the road to an integrated map. Plant Physiol 130: 1598-1605.

Yim YS, Davis GL, Duru NA, Musket TA, Linton EW, Messing JW, McMullen MD, Soderlund CA, Polacco ML, Gardiner JM and
Coe EH Jr. (2002) Characterization of three maize bacterial artificial chromosome libraries toward anchoring of the physical map
to the genetic map using high-density bacterial artificial chromosome filter hybridization. Plant Physiol 130: 1686-1696.

Swigonova Z, Lai J, Ma J, Ramakrishna W, Llaca V, Bennetzen JL and Messing J (2004) Close split of sorghum and maize genome
progenitors. Genome Res 14: 1916-1923.

Lai J, Ma J, Swigonova Z, Ramakrishna W, Linton E, Llaca V, Tanyolac B, Park Y-J, Jeong O-Y, Bennetzen JL and Messing J (2004) Gene loss and movement in the maize genome. Genome Res 14: 1924-1931.

Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL,
SanMiguel P, Lakey N, Bedell J, Yuan Y, Budiman MA, Resnick A, Van Aken S, Utterback T, Riedmuller S, Williams M,
Feldblyum T, Schubert K, Beachy R, Fraser CM and Quackenbush J (2003) Enrichment of gene-coding sequences in maize by
genome filtration. Science 302: 2118-2120.

Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei F, Fuks G, Soderlund C, Mayer KFX and Wing RA (2004) Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 101: 14349-14354.

PGIR HICF & BES team: Arvind K. Bharti, Steve Young, Steve Kavchok, Gladys Keizer, Amy B. Nelson, Valerie Zohovetz, Galina Fuks and Joachim Messing

AGI HICF team: Ed Butler, Jose L. Goicoechea, Stephanie DeVito, Elena Ruiz, Danielle Yost and Rod A. Wing
AGI BES team: HyeRan Kim, Yeisoo Yu, Diana Stum and Rod A. Wing
AGCol team: William M. Nelson, Jamie Hatfield and Carol A. Soderlund
MIPS annotation team: Heidrun Gundlach, Georg Haberer, Wojciech M. Karlowski and Klaus F.X. Mayer
Broad Ins. BAC sequencing team: Sarah Towey, Christina Raymond, Steve Rounsley, David Jaffe, Chad Nusbaum and Bruce Birren

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