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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

2008 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
Since April of 2008, the MaizeGDB team: worked with the Maize Genome Sequencing Consortium personnel to make information about the project to sequence B73 accessible to researchers and added significant data (including but not limited to reference, map, map scores, insertional mutant, locus, and sequence information for a subspecies of Zea) to the database. A major project to create a Genome Browser for MaizeGDB has been undertaken to enable researchers to browse sequence data via MaizeGDB and to serve as a central organizer for MaizeGDB’s transition to a more sequence-centric resource. Choice of browser software (GBrowse) is based upon information provided by stakeholders. The MaizeGDB Genome Browser’s release is anticipated to take place in early September. 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. The research carried out by the MaizeGDB Team relates to NP 301, Component 2 by creating data and informatic resources for maize genetics and genomics researchers.


4.Accomplishments
1. 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. This work is a part of NP 301, Program Component 2. The problem statement that is best addressed by this work is Problem Statement 2A: Genome Database Stewardship and Informatics Tool Development.

2. MaizeGDB’s Genome Browser software was selected.

MaizeGDB must evolve into a more sequence-centric resource to meet the needs of stakeholders. To that end, a genome browser will be incorporated into the MaizeGDB product. Various softwares are available for genome browsers, and they all have different functionality. The Maize Genetics Executive Committee charged MaizeGDB personnel with surveying the community to find out which types of functionalities researchers wish to utilize for genome browsing. The survey was conducted, and information gained from that survey was utilized to select the software best suited to meet stakeholders’ expressed needs. GBrowse software was selected as the software for the MaizeGDB Genome Browser. Stakeholders will have more functionalities specific to their research needs and they will be enabled to better interact with the B73 sequence information. This work is a part of NP 301, Program Component 2. The problem statement that is best addressed by this work is Problem Statement 2A: Genome Database Stewardship and Informatics Tool Development.

3. Chromatin Consortium and TILLING data available via MaizeGDB.

Data generated by the Chromatin Consortium and the TILLING project are deposited in an online repository that will not be available once NSF funding for those projects ends. By working alongside personnel from the Chromatin Consortium and the TILLING project, pipelines to transition these highly utilized datasets and materials to MaizeGDB for long-term storage and access were created. Researchers currently using the mutants and related data generated by these projects as well as those who will want to use these resources in the future will be able to access these data at MaizeGDB. This work is a part of NP 301, Program Component 2. The problem statement that is best addressed by this work is Problem Statement 2A: Genome Database Stewardship and Informatics Tool Development.

4. Phenotype lists for use in the field were created and made accessible online, and community members were encouraged to use these lists for screening fields.

Maize researchers use various terms to describe the same phenotype, which causes curation problems when the data are integrated into an online repository. As an initial step toward creating data capture methods to be used in the field, the phenotypic terms at MaizeGDB were dumped to lists for researchers to use in their fields. By having the MaizeGDB phenotypic terms in hand, researchers are likely to annotate their phenotypic data using these terms rather than idiosyncratic sets of terms unique to a given lab group. This makes it possible to integrate the data into MaizeGDB without time spent converting the terms to the MaizeGDB vocabulary, which requires a serious investment of time. This initial interaction with community members to document phenotypes is an initial step in a plan to make data capture via hand-held devices using MaizeGDB’s information possible in the 2009 field season. This work is a part of NP 301, Program Component 2. The problem statement that is best addressed by this work is Problem Statement 2A: Genome Database Stewardship and Informatics Tool Development.


5.Significant Activities that Support Special Target Populations
The MaizeGDB Team mentored three American Indian students for a program that aims to increase their representation in the sciences.


6.Technology Transfer

Number of Web Sites Managed1
Number of Non-Peer Reviewed Presentations and Proceedings1

Last Modified: 4/20/2014
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