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United States Department of Agriculture

Agricultural Research Service

Research Project: AN INTEGRATED DATABASE AND BIOINFORMATICS RESOURCE FOR SMALL GRAINS
2008 Annual Report


1a.Objectives (from AD-416)
1) Integrate small grains genetic and genomic data within the GrainGenes database and link to relevant external databases;.
2)Develop software and interfaces to enhance utility for researchers.


1b.Approach (from AD-416)
1) Extend development and curation within the GrainGenes project to include a suite of integrated databases and web-based resources for wheat, barley, rye, triticale, and oats research and improvement. .
2)Carry out projects involving direct and collaborative support to those aspects of small grains genomics/genetics/molecular biology relevant to crop improvement..
3)Target user needs through meetings, personal interactions, and electronic communication with the small grains research community. .
4)Develop improved displays and tools needed for improvement of the GrainGenes database and its inter-connections to other bioinformatics projects. Previously 5325-21000-007-00D (7/03). Replacing 5325-21000-010-00D (04/08). BSL-1 (4/08).


3.Progress Report
The project has developed a system for online submission of research proposals to be considered for funding by the US Wheat and Barley Scab Initiative. The system provides submitters and reviewers with secure access to the files they have access to, and tracks proposals through the approval process.

The Genomic Diversity and Phenotype Connection (GDPC, www.maizegenetics.net/gdpc) can connect to and extract data from several disparate relational databases using different schemas. A GDPC adapter has now been built that works with the Wheat CAP database described above, allowing the user to retrieve SSR and SNP molecular allele data for a desired set of germplasm accessions and markers.

Recently a web-based interface has been developed to provide a database conversion and administration tool for the Comparative Map Viewer (CMap, http://rye.pw.usda.gov/cmap) data. Most of this data is extracted from the GrainGenes database, with the rest provided by curator input. This interface greatly streamlines a routine operation in database maintenance.

NP 301 Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statements A: Genome Database Stewardship and Informatics Tool Development, B: Structural Comparison and Analysis of Crop Genomes, and C: Genetic Analyses and Mapping of Important Traits.


4.Accomplishments
1. Integrating genetic and physical maps with developing genomic sequences. Increasing amounts of small grains genomic and EST sequences will be maximally utilized only when integrated with available genetic and physical maps of these species. As genomic sequencing and physical mapping of Triticeae scale up, there is a need to integrate with core grass model systems Brachypodium and rice. The project refined and solidified protocols for collecting map data and displaying it in a user-friendly online format that enables comparing maps with each other. The physical map of the wheat relative Aegilops tauschii was integrated with four wheat genetic maps by use of common markers. Five genetic maps of barley and three of wheat were added to the database, bringing the total number to 172. A summary table of the maps is available at http://wheat.pw.usda.gov/ggpages/map_summary.html. It now includes a short list of the most important maps, as an aid to users who are not familiar with the full range of maps available.

NP 301 Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statements B: Structural Comparison and Analysis of Crop Genomes and C: Genetic Analyses and Mapping of Important Traits.


5.Significant Activities that Support Special Target Populations
None.


6.Technology Transfer

Number of New Patent Applications Filed1
Number of Web Sites Managed6
Number of Non-Peer Reviewed Presentations and Proceedings3

Last Modified: 10/24/2014
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