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.
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.
Integration of genome sequence with genetic information. The traits that are mapped to the genome are often mapped using genetic map units (centimorgans) whereas genomics information is mapped in base pairs. To make use of traits information simultaneously with genomics data, these two measures of information must be integrated. ARS researchers in Ames, IA, Columbia, MO, and Albany, CA in collaboration with researchers at Iowa State University have mapped genetically defined regions of the genome to the genome assembly and made the resulting information available via Maize Genetics and Genomics Database (MaizeGDB). Not only can a researcher now look at a particular region of the genome sequence assembly and know the position of a region on genetic maps, it is also now possible to measure how many generations it would take to create recombinations that stack useful, mapped traits. These tools are available via the MaizeGDB Genome Browser at http://gbrowse.maizegdb.org/gb2/gbrowse/maize_v2/, and serve as a practical tool for corn genetic improvement.
New DNA-based markers made available for crop improvement. Newly documented DNA sequence variations, which serve both as markers and as the raw materials for breeding, are now available alongside phenotypic descriptions for genomic analyses to effect crop improvement. ARS researchers in Ames, IA, Columbia, MO, Ithaca, NY, and Albany, CA in collaboration with researchers at Iowa State University have integrated into Maize Genetics and Genomics Database (MaizeGDB) the genetically mapped genotypic and phenotypic data for the Nested Association Mapping (NAM) lines. NAM lines and their phenotypic data comprise a powerful tool that is now used by many researchers to decipher how the genome sequence encodes favorable traits. These lines encompass the range of maize diversity by including temperate, tropical, sweet corn and popcorn lines. This mapping population is publicly available from the USDA ARS Maize Genetics Cooperation – Stock Center, Champagne-Urbana, IL. Genotype data are available now via the MaizeGDB Genome Browser. Phenotype data are currently accessible at the Ithaca, NY Diversity project site, http://www.panzea.org. The integration of these data into MaizeGDB adds more facile access to other sequence-based functional data, which include a gene expression atlas and predicted metabolic pathways involvement for the gene models. Plant researchers and breeders alike benefit from the availability of these data.
Predicting how gene function helps researchers create crop improvement strategies. Gene function predictions are now mapped to the genome and are available via Maize Genetics and Genomics Database (MaizeGDB). ARS researchers in Ames, IA, Columbia, MO, Albany, CA, and Ithaca, NY in collaboration with researchers at Iowa State University and the University of Oregon have added predicted information about maize gene function based upon the known function of the same genes in other species. This information enables researchers to know enough about how a gene may function to generate reasonable, testable hypotheses and quickly move from the computer to the lab bench and field to determine how genes may function in the plant to effect crop improvement.
How genes function in the cell is now documented and can be visualized. Maize Genetics and Genomics Database's (MaizeGDB) pathway view tool suite now includes a small, quality dataset as well as a higher-coverage, more experimental version. ARS researchers in Ames, IA, Columbia, MO, Albany, CA, and Cold Spring Harbor, NY in collaboration with researchers at Iowa State University, Oregon State University, and Stanford University have deployed two pathway view tools: CornCyc and MaizeCyc. Both are useful to decipher the metabolic pathways and gene product interactions encoded by the B73 reference genome sequence. Both rely on predicted and experimentally confirmed pathway information. MaizeCyc is a larger dataset whereas CornCyc is a smaller, validated and quality checked resource. These resources provide a view of how gene products function to help researchers determine which genes and/or biochemical pathways might be good targets for crop improvement.
Maize researchers can now see where genes function. ARS researchers in Ames, IA, Columbia, MO, and Albany, CA in collaboration with researchers working at Iowa State University, the University of Toronto in Canada, and the Max-Planck-Institut für Molekulare Pflanzenphysiologie in Potsdam, Germany have released views of the “electronic Fluorescent Pictograph” browser that demonstrate regions of the plant where genes are expressed as well as views from the MapMan tool that compare genome-wide gene expression across two or more tissues and/or experiments. The visualization tools, now embedded in the USDA-ARS Maize Genetics and Genomics Database (MaizeGDB) interface, enable researchers to quickly comprehend how and where gene products function to determine targets for improvement and enable plant improvement through altering gene expression patterns.
Maize Genetics and Genomics Database (MaizeGDB) full website redesign. ARS researchers in Ames, IA, Columbia, MO, and Albany, CA in collaboration with researchers at Iowa State University have improved the look and feel of the new, pre-release (alpha) MaizeGDB website. It is more modern, the technologies are updated to modern software and systems, the database is separated from the interface (which will enable a facile near future transition from an expensive database system to an open source and inexpensive alternative) and the design enables access to data stored off-site from within a context-appropriate site. The alpha release is now available (where alpha indicates that the site is a work in progress) at http://alpha.maizegdb.org/. MaizeGDB makes accessible genetic and genomic data and data analysis tools that are used by researchers to investigate basic biological concepts and translate finding into technology that is deployed in farmer's fields.
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.