Honors Program: Iowa State University

Project Name: Cracking the Corn Genome Code

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Has your project helped those it was designed to help?   Yes.

What new advantage or opportunity does your project provide to people?

The project enabled researchers in agricultural genomics and biorenewable research involving manipulating plants, especially maize, at the genomic level. With advances in biotechnology, almost every endeavor -- such as increasing yield, creating improved varieties of corn, improving nutrition such as increasing vitamin content and increasing value for biorenewable fuel production -- all rely on genome-level understanding, and understanding the complex interactions between genes and gene products, as the underlying basis. The project shortcuts the time required for going from raw data to analyzed information from several months to the span of several hours to a few days. This time reduction also allows running the software with multiple parameters, to create a more robust analysis. The Iowa State team has even been able to build custom assemblies upon request and deliver them to users, which is a major paradigm shift in assembly capability. The maize genome assembly carried out by the Iowa State team has been made available at http://www.plantgenomics.iastate.edu/maize (Appendix 1). This site has been used by thousands of researchers (see Appendix 3 for accesses over several weeks; note that once a researcher downloads the entire assembly, he/she can carry out the investigation in-house and does not need to come back to the Web portal). There is a high degree of satisfaction in the quality of the assembly provided, and several researchers have made remarks about how this empowered their research.

The project provides two significant benefits: It enables speedy discovery of genomes, and carries out other types of large-scale DNA sequence analysis, which will form the foundation supporting research in many aspects of biotechnology for decades to come. It also enables other groups, which can use the PaCE software to carry out large-scale DNA sequence analysis that suits their needs and applications.

Has your project fundamentally changed how tasks are performed?   Yes.

How do you see your project's innovation benefiting other applications, organizations, or global communities?

The PaCE software has been used by over 50 groups from 11 different countries: the U.S., Australia, Austria, Brazil, China, Germany, India, Ireland, Korea, Netherlands and Taiwan. The users include governmental research agencies, nonprofit research organizations, academic research institutions and commercial entities. It has been used in many different applications, most notably in analyzing large collections of DNA sequences derived from active genes. The NSF-funded plant genome Web portal, PlantGDB, a comprehensive resource for plant genome information, uses this software to carry out such analysis. The software can benefit many applications by grouping related DNA sequences efficiently, following which specific application-dependent analysis can be performed. For example, one can group related DNA sequences from several individuals, and then look for single base differences that could potentially be the cause for genetically inherited diseases.

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