Maize Genome Consortium


Maize Genomics Consortium is one of the projects sponsored by NSF (see the other project "Sequencing the Maize Genome"). It exploits the differences between the low-copy sequence fraction of the maize genome thought to contain the genes, and the highly abundant repetitive fraction. This project is being conducted by a team consisting of Karel Schubert, Roger Beachy and Brad Barbazuk at the Danforthcenter, Cathy Whitelaw and John Quackenbush at TIGR, Jeff Bennetzen at Purdue University, and Orion Genomics.

The Key features of this project are:

1.) Develop and evaluate two strategies to isolate and sequence the maize gene space.

These strategies are: The Maize Genomics Consortium will produce up to 500,000 sequence reads from clones from libraries constructed from each of these promising methods. The information contained in these reads will allow the Maize Genomics Consortium to:

2.) Determine the gene hit rate, gene space coverage and biases of both methods, and disseminate all data into the public domain.

This will allow the Maize Genomics Consortium to properly evaluate these methods and recommendation a strategy for completing the maize genome sequence.

Progress for this project and deliverables are available from the maize genome project web pages hosted at the Donald Danforth Plant Science Center, and TIGR. Sequence reads are generated at TIGR and deposited into GenBank. The sequences are also available for download from the TIGR maize FTP site.


Methyl-filtration, a technique licensed to Orion Genomics, exploits the finding that the majority of retrotransposon and repetitive sequences in maize are methylated.

Plant genomes are comprised of ISLANDS of genes nestled among OCEANS of repetitive junk DNA.



The repetitive DNA is comprised mostly of retrotransposon elements that are heavily methylated (red bars), while genes (black arrows) are not methylated.

With the GeneThrsher® approach...


...genomic subclones are generated by fragmenting DNA from the plant of interest.



The resulting library primarily contains the genespace and reduces the size of complexity of the genome.

 High Cot selected libraries produced by Jeff Bennetzen at Purdue University exploit the relatively low abundance of the gene sequences, which are present in small number of copies in the genome.

High Cot

  • DNA from immature maize ears sheared to an average size of 1.0 to 2.0 kb
  • Sheared DNA is denatured and then renatured to a C0t value of 800
  • Unrenatured DNA is purified over a HAP column
  • ssDNA converted to dsDNA
  • dsDNA size selected to 1.2 to 2.0 kb
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