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United States Department of Agriculture

Agricultural Research Service

Research Project: THE MAIZE GENETICS AND GENOMICS DATABASE

Location: Corn Insects and Crop Genetics Research

2009 Annual Report


1a. Objectives (from AD-416)
Objective 1: Integrate new maize genetic and genomic data into the database. Objective 2: Provide community support services, such as lending help to the community of maize researchers with respect to developing and publicizing a set of guidelines for researchers to follow to ensure that their data can be made available through MaizeGDB; coordinating annual meetings; and conducting elections and surveys.


1b. Approach (from AD-416)
Data integration: To best leverage the cooperative spirit of the maize community, we will encourage the use of a set of Community Curation Tools to enable researchers to deposit their own small datasets into the database directly. To reduce secondary curation of data, we will generate standards for data deposition and define file formats for automated inputs of large datasets and will work in concert with maize researchers as they devise methods for initial data storage so that the data transition to MaizeGDB is simplified. Shift to a sequence-centric paradigm: To allow researchers to visualize a gene within its genomic context and to visualize gene products within the context of relevant metabolic pathways annotated with ontology terms, we will develop new views of the data. We will link sequence data to relevant datasets, especially the centrally important maps such as (1) IBM2, (2) its neighbors, and (3) the new maize diversity map. We also will incorporate a genome browser into the MaizeGDB product to create a view that includes all major genome assemblies and predicted gene structures and displays the official maize genome annotation. Community coordination: We will conduct critical maize genetics community functions including coodinating and conducting annual meetings, elections, and surveys and preparing the Maize Newsletter.


3. Progress Report
Over the course of FY09, the MaizeGDB team worked with the Maize Genome Sequencing Consortium personnel to make information about the project to sequence inbred line B73 accessible to researchers. In addition, information describing comparisons between B73 and inbred line Mo17 (also being sequenced) were brought into MaizeGDB from the Department of Energy’s Joint Genome Institute. Project personnel added significant data (including but not limited to reference, map, map scores, insertional mutant, locus, gene model, and sequence information for all subspecies of Zea) to the database. A major project to create a Genome Browser for MaizeGDB has been completed to enable researchers to browse sequence data via MaizeGDB and serves as the centerpiece for MaizeGDB transition to a sequence-centric resource. The Genome Browser’s associated Locus Lookup Tool was invented and has been released allowing researchers to identify regions of the genome where genes of interest may lie based upon physical and genetic map data. Work carried out by the MaizeGDB team has resulted in improved communication among maize researchers, increased ability to document the results of experiments, and increased availability of information relative to high impact research.


4. Accomplishments


5. Significant Activities that Support Special Target Populations
During the summer months of FY09, the MaizeGDB Team mentored four American Indian students for a program that aims to increase their representation in the sciences.


Review Publications
Gray, J., Bevan, M., Brutnell, T., Buell, C., Cone, K., Hake, S.C., Jackson, D., Kellogg, E., Lawrence, C.J., Mccouch, S., Mockler, T., Moose, S., Paterson, A., Peterson, T., Rokshar, D., Souza, G., Springer, N., Stein, N., Timmermans, M., Wang, G., Grotewold, E. 2009. A Recommendation for Naming Transcription Factor Proteins in the Grasses. Plant Physiology. 149(1):4-6.

Yi, G., Luth, D., Goodman, T.D., Lawrence, C.J., Becraft, P.W. 2009. High-throughput Linkage Analysis of Mutator Insertion Sites in Maize. Plant Journal. 58(5):883-892.

Last Modified: 10/16/2017
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