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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

2011 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
ARS scientists working on the Maize Genomic 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. Most notably, the expression of maize genes across 60 tissue types and developmental stages was mapped to the genome sequence in a way that researchers can quickly determine the relative expression of genes across various tissues and treatments. MaizeCyc, another resource that has been developed and deployed, allows the gene set of maize to be mapped to highly curated metabolic pathways to determine how expression of genes contributes to phenotypes. At this time, all major published recombination-based genetic maps have been brought into the MaizeGDB resource. The data management and display system called ZeAlign now coordinates integration of individual investigator data with the deluge of next generation sequencing data and prepares such datasets for automatic upload to the MaizeGDB Genome Browser. We continue to develop and use controlled vocabularies and ontologies to describe developmental, growth, and anatomic aspects of visible phenotype trait variation and also, new this year, to apply these to molecular gene expression data. In addition, personnel have put in place an infrastructure that ensures that MaizeGDB will always be available for researchers' use. 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 monitored by meetings, phone calls, and e-mail communications.


4. Accomplishments


Review Publications
Yennamalli, R.M., Rader, A.J., Wolt, J.D., Sen, T.Z. 2011. Thermostability in endoglucanases is fold-specific. BMC Structural Biology. 11(10):1-15.

Lawrence, C.J. 2011. MaizeGDB - Past, present, and future. Maydica. 56(1):1-3.

Green, J.M., Harnsomburana, J., Schaeffer, M.L., Lawrence, C.J., Shyu, C. 2011. Multi-source and ontology-based retrieval engine for maize mutant phenotypes. Database: The Journal of Biological Databases and Curation. 2011:Article ID bar012. Available: http://database.oxfordjournals.org/content/2011/bar012.

Schaeffer, M.L., Harper, E.C., Gardiner, J.M., Andorf, C.M., Campbell, D.A., Cannon, E.K., Sen, T.Z., Lawrence, C.J. 2011. MaizeGDB: Curation and outreach go hand-in-hand. Database: The Journal of Biological Databases and Curation. 2011:Article bar022. Available: http://database.oxfordjournals.org/content/2011/bar022.long.

Harper, E.C., Schaeffer, M.L., Thistle, J., Gardiner, J., Andorf, C.M., Campbell, D.A., Cannon, E.K., Braun, B.L., Birkett, S., Lawrence, C.J., Sen, T.Z. 2011. The MaizeGDB Genome Browser Tutorial: One example of database outreach to biologists via video. Database: The Journal of Biological Databases and Curation. DOI: 10.1093/database/bar016:1.

Last Modified: 10/19/2017
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