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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

2012 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 coordinating and conducting annual meetings, elections, surveys and preparing the Maize Newsletter.


3. Progress Report:
ARS scientists working on the Maize Genetics and Genomics Database (MaizeGDB) in Ames, IA, Columbia, MO, and Albany, CA worked to improve tools that make the maize genome sequence useful for investigative researchers. Project personnel added significant data (including but not limited to reference maps, map scores, insertional mutant, locus, gene model, and sequence information for all subspecies of maize) to the database. Researchers were trained in the use of the MaizeGDB website at Stanford, CA as well as at the Annual Maize Genetics Conference in Portland, OR where more than 70 university, government and industry scientists attended an intensive “how-to” workshop. MaizeGDB personnel also managed the Annual Maize Genetics Conference abstract submission, meeting program compilation, and IT services. Work carried out by the MaizeGDB team has resulted in improved communication among maize researchers worldwide, increased ability to document the results of experiments, and increased availability of information relative to high impact research. Collaborations are being supported by meetings, phone calls, and e-mail communication.


4. Accomplishments


Review Publications
Harper, E.C., Sen, T.Z., Lawrence, C.J. 2012. Plant cytogenetics in genome databases. In: Bass, H.W., Birchler, J.A., editors. Plant Cytogenetics. New York, NY: Springer. p. 311-322.

Cannon, E.K., Birkett, S.M., Braun, B.L., Kodavali, S., Jennewein, D.M., Yilmaz, A., Antonescu, V., Antonescu, C., Harper, E.C., Gardiner, J.M., Schaeffer, M.L., Campbell, D.A., Andorf, C.M., Andorf, D., Lisch, D., Koch, K.K., McCarty, D.R., Quackenbush, J., Grotewold, E., Lushbough, C.M., Sen, T.Z., Lawrence, C.J. 2011. POPcorn: An online resource providing access to distributed and diverse maize project data. International Journal of Plant Genomics. 2011:Article 923035. Available http://www.hindawi.com/journals/ijpg/2011/923035.

Last Modified: 10/17/2017
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