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.
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.
MaizeGDB’s Genome Browser was released. MaizeGDB must evolve into a more sequence-centric resource to meet the needs of stakeholders. To that end, a genome browser was incorporated into the MaizeGDB product. GBrowse was configured for MaizeGDB specific to requests made by stakeholders. Data from GenBank, MaizeSequence.org, PlantGDB, MAGI, PLEXdb, UniformMu, and others were loaded onto the same frame to allow researchers to visualize and interact with the B73 genome sequence (example at http://gbrowse.maizegdb.org/cgi-bin/gbrowse/maize/). Researchers can use the maize genome sequence to further their research.
The Locus Lookup Tool at MaizeGDB was invented and released. Methods to automatically integrate sequence information with physical and genetic maps are needed by researchers but are entirely absent from the bioinformatics toolbox. MaizeGDB team members invented the Locus Lookup Tool for maize. This tool enables researchers to define windows of genomic sequence likely to contain loci of interest where only genetic or physical mapping associations are documented, and can be adapted to other biological systems. Researchers can find regions of the genome likely to contain genes of interest for which no sequence data are available. This allows researchers to leverage the B73 genome sequence even if their gene of interest is not cloned.
The POPcorn Project Portal has been released. Maize researchers cannot easily leverage all available genetic and genomic data because the online locations of all resources are not easy to find, and the sequence-indexed resources generated by individual projects must be searched independently. In addition, it is often the case that when a project’s funding period ends, the generated data are lost because they are not moved to long-term repositories, and these once-funded project sites degrade over time and sometimes disappear entirely. POPcorn overcomes these challenges in collaboration with the community of maize researchers by launching POPcorn (PrOject Portal for corn), a needs-driven resource and data pipeline. POPcorn currently makes available (1) a centralized Web-accessible resource to search and browse ongoing maize genomics projects. Over the course of the coming year, (2) a single, stand-alone tool that makes use of Web services and minimal data warehousing to enable researchers to carry out sequence searches at one location that return matches for all participating projects’ related resources, and (3) a set of tools that enable collaborators to migrate their data to MaizeGDB, the long-term model organism database for maize genetic and genomic information (to be added at their projects’ conclusion). POPcorn aids in the identification of the molecular-level phenotypes manifesting as traits that plant breeders select for and will lead to improvements in food, fuel, and nutrition.
UniformMu data available via MaizeGDB. The locations of inserted DNA that cause mutations are obvious relative to genomic context. If locations are known, researchers could know whether a gene of interest is tagged by an insertional mutant and could request seed for plants carrying tagged mutations. By working alongside personnel from the UniformMu project, pipelines to transition these highly utilized datasets and materials to MaizeGDB for long-term storage and access were created. Researchers interested in finding out whether there is a Mutator insertion in a gene of interest can now find the data at MaizeGDB, thus enabling them to order seed stocks and determine the function of agronomically important genes.
MaizeGDB provides access to B73 sequencing project information and materials. Maize researchers need access to information describing the status of the project to sequence B73 in order to plan and conduct sequence-based research. The Maize Genome Sequencing Consortium’s reports, PowerPoint presentations, and lists of materials utilized in the sequencing efforts were posted and kept up-to-date at MaizeGDB (see http://www.maizegdb.org front page as well as http://www.maizegdb.org/sequencing_project.php). Maize researchers can access descriptions of the sequencing effort as well as maize sequences via MaizeGDB, thus enabling them to utilize the maize genome sequence alongside other genetic and genomic information to further their research.
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.
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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.