ARS | Publication request: DEVELOPMENT OF AN INTEGRATED LABORATORY INFORMATION MANAGEMENT SYSTEM FOR THE MAIZE MAPPING PROJECT

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 3, 2003
Publication Date: November 1, 2003
Citation: SANCHEZ-VILLEDA, H., SCHROEDER, S., POLACCO, M.L., MCMULLEN, M.D., HAVERMANN, S., DAVIS, G., VROH, B.I., CONE, K., SHAROPOVA, N., YIM, Y., SCHULTZ, L., NGOZI, D., MUSKET, T., HOUCHINS, K.E., FANG, Z., GARDINER, J., COE JR, E.H. DEVELOPMENT OF AN INTEGRATED LABORATORY INFORMATION MANAGEMENT SYSTEM FOR THE MAIZE MAPPING PROJECT. BIOINFORMATICS. 2003. V. 19(16). P. 2022-2030.

Interpretive Summary: The development of an integrated genetic and physical map for the maize genome involves the generation of an enormous amount of data and database programs to manage the data. An integrated informatics system has been derived to aid in research with all the different types of markers coming from both local and remote users. In addition, the system interacts with mapping tools and with data from sequencing instruments. The Laboratory Information Management System developed for the Maize Mapping Project (http://www.maizemap.org/) is currently used successfully in a high-throughput mapping environment. The system is flexible and can easily be modified to manage data for other species. The software is freely available at http://www.maizemap.org/bioinformatics.htm. Application of this system to maize and to other species enhances the ability not only to compile and systematize data; it also ensures that very substantial investments in genomics research are documented, stored, and made accessible for verifications, and for further research and analysis. The design and production of this data system advances the goals of researchers conducting genomic research on crops: to increase their productivity and quality, and to garner knowledge that can lead to new applications of added value and sustainability.

Technical Abstract: The development of an integrated genetic and physical map for the maize genome involves the generation of an enormous amount of data. Managing this data requires a system to aid in genotype scoring for different types of markers coming from both local and remote users. In addition, the system must be able to interact with mapping tools and with data from sequencers. The system is also required to be able to generate potential primers for use in mapping and to provide views of the integrated physical and genetic map and comparisons of genetic maps. The MMP-LIMS system is currently used successfully in a high-throughput mapping environment. Over 900 SSR markers, more than 890 RFLP markers, over 130 SNPs, and over 80 InDels have been entered and verified via MMP-LIMS. The system is flexible and can easily be modified to manage data for other species. The software is freely available. For iMap and cMap software, please fill out the form on our website. The other MMP-LIMS software is available at http://www.maizemap.org/bioinformatics.htm.