Progress Towards Sequencing the Maize Genome

Jeff Bennetzen
Department of Biological Sciences
Purdue University
West Lafayette, IN

Starting in June of 2000, the Maize Genetics Executive Committee (MGEC) began discussing possible visions for the future of maize genetics. From these discussions, it became clear that the landscape for plant genetics research had changed tremendously in the preceding year, and that the time was now right to support an effort to sequence the maize genome. A strong majority of the MGEC proposed that this should be the highest current priority for maize genetics research.

The MGEC prepared an executive summary and a more detailed document that included a number of outlined possible priorities for maize genetics over the next few years. These documents were disseminated electronically to the entire maize genetics community and were also discussed by attendees in an open forum at the 2001 Maize Genetics Meeting. From this feedback, the community voiced its opinion that sequencing the maize genome deserved the highest priority.

A subset of the MGEC, Jeff Bennetzen, Vicki Chandler and Pat Schnable, organized a one-day workshop in St. Louis (July 2, 2001) to discuss how the maize genome might best be sequenced. A grant was funded by NSF to support this meeting. To make the meeting manageable, only 28 scientists were invited. These scientists included experts in maize genome analysis, informatics, and full genome sequencing from the public, private and federal sectors, including overseas representatives. Discussion subjects included the techniques that should be pursued, the availability of sufficient sequencing capacity, how the information would be disseminated, predicted costs, and possible timeframes.

The results of this meeting were the concurrence that sequencing the maize genome is completely feasible, and that the whole project could be accomplished in one to two years at a cost of $20 million to $100 million. The great variation in possible costs reflects the diversity of techniques that could be pursued and the degree of sequence redundancy that would be generated. At the moment, there is enthusiasm among animal geneticists for producing "drafts" in many projects to sequence higher eukaryotic genomes. Because a draft sequence is at a relatively low redundancy (3X to 6X, usually), it is impossible to assemble final sequences that are very long, but most gene sequences are identified. The draft costs less and can be produced more rapidly than a complete sequence. The final costs to finish the sequence can dwarf the cost of the draft.

The most controversial subject at the workshop was the sequencing strategy that should be employed. Most participants felt that a gene-enriched sequencing approach should be pursued initially, thus providing the most important targets at an early time and a relatively low cost. The gene-enrichment technologies discussed included various shotgun approaches based on the low methylation level of maize genes, their low repetition frequency, the lack of stop codons in their coding regions, or the proximity of DNA transposons. Two participants felt that the sequencing of BACs from gene-rich regions would be most appropriate. Several of the industrial participants felt that a full genome shotgun sequence should be employed. In all of these cases, there were questions of whether all genes would be found and of how difficult it would be to assemble this sequence information. All participants agreed that, for an acceptable final result, the sequence must be unambiguously and precisely ordered on the physical and genetic maps of maize. How best to do this, and thus how best to undertake the full genome sequencing process, appeared to require additional studies that could be completed within a few months time.

Bennetzen, Chandler and Schnable produced a summary of the outcomes and proposed next steps from this meeting. This report has been disseminated to federal funding agencies, the National Corn Growers Association and the maize genetics community. Representatives of all three of these groups have voiced their interest in sequencing the maize genome. The National Corn Growers Association has placed sequencing of the maize genome at the top of its priority list for 2001 - 2002.

The MGEC will continue to monitor and encourage steps towards sequencing the maize genome by the most appropriate method. We hope that this project will initiate in 2002 and be completed within two years of that start date.

Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors.

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