Honors Program: Iowa State University

Project Name: Cracking the Corn Genome Code

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Success

Has your project achieved or exceeded its goals?   Exceeded.

Is it fully operational?   Yes.

How many people benefit from it?   1,000-plus.

If possible, include an example of how the project has benefited a specific individual, enterprise or organization. Please include personal quotes from individuals who have directly benefited from your work.

The project achieved the original goal of creating software that can process large DNA collections and, in particular, assemble maize and other complex plant genomes. Recently, it has also been applied to assemble sorghum. The project induced a paradigm shift in agricultural genomics research -- the project changed assemblies from a difficult task carried out by teams of computer scientists over several months to a task within the reach of a biological investigator or an experienced graduate student. An important outcome of this great speed and ease is the ability to carry out assemblies with multiple parameters. When assembly is a difficult task spanning months, the results had to be used unchallenged. Now, the assembly can be redone with multiple parameters to generate a more robust result. One can also generate conservative assemblies using a stringent set of parameters and similarly obtain more information with some risk of inaccuracy using a liberal parameter set. The use of the software by 50 research groups worldwide, and its use in other large-scale applications, has exceeded the goals set for the project.

Some comments by researchers benefiting from this project are included below. MAGI stands for Maize Assembled Genomic Island, a term that denotes a piece of the assembly (see Appendix 3).

Using your databases, we have been able to identify homologs/orthologs that play a critical role in phytoalexin biosynthesis -- Surinder Chopra, associate professor, Pennsylvania State University

Before MAGI was available, our success rate was never more than 15% for all the databases combined. Thanks to MAGI, our success rate has gone up to 70% -- Guri Johal, associate professor, Purdue University

Remarkably complete. We found 32 of the predeicted ~35 members of cellulose synthase-like gene family. Very pleased with the quality of the data. -- Jonathan Walton, professor, Michigan State University

How quickly has your targeted audience of users embraced your innovation? Or, how rapidly do you predict they will?

The innovation has two types of targeted audience: One is maize geneticists and the other is agricultural researchers who can use our assembly in their own research. The results of our assembly, upon due verification, have been made accessible via a Web portal developed for this task, http://www.plantgenomics.iastate.edu/maize. An e-mail was sent out to many in the targeted audience through e-mail lists and other forums. The assembly has been instantaneously embraced by the target community as witnessed by hundreds of downloads and analysis requests recorded by the Web site. Users could either download complete assembly to their desktops or search the assembly at the Web site using the popular BLAST search engine. Both of these have been widely used immediately upon release. The second type of target audience is bioinformatics and other researchers interested in using our software. This has seen a good degree of acceptance as witnessed by the number and geographic diversity of the user community and the variety of problems to which it has been applied. It should be kept in mind that the innovation is targeted only toward the high-end users -- while the software will work equally well on small data sets, there are many other solutions that can easily take care of smaller problems. While fewer teams carry out large-scale sequencing projects, many nationally and internationally important projects fall in this category. Future efforts will be targeted to improving the flexibility and functionality of the software to increase its ease of use and adoption.

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