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United States Department of Agriculture

Agricultural Research Service

Research Project: AN INTEGRATED DATABASE AND BIOINFORMATICS RESOURCE FOR SMALL GRAINS
2009 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).


3.Progress Report
The entire website for the US Wheat and Barley Scab Initiative was converted into a module style PHP administrated website, adding efficiency toward adding updates to the website. A system for online submission of research proposals also allows submitters and reviewers to track proposals through the approval process with secure access to the files they have access to.

Curator processing of small grains research information allowed genetic and physical maps to be integrated into the GrainGenes resource. For barley, diversity SNP consensus maps for pilot and extended projects, and two additional population studies were added. For wheat, new marker technologies including DArT, SSR, and MAS (expressed STSs/SSRs) have added new maps, including one from the wheat CAP project, and an updated map from the NSF-funded wheat physical mapping project. Additional maps included a rye consensus map and a 21 linkage group map for hexaploid oat. Assistance was also provided to Brachypodium and switchgrass research projects to build development maps which will be incorporated into future database resources.

Advancements were made toward improving administrative interfaces for the database and software tools. Recently a web-based interface was developed to provide a database conversion and administration tool for the Comparative Map Viewer (CMap, http://wheat.pw.usda.gov/cmap) data, a critical interface for viewing map 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. Weekly updates of the GrainGenes database have been facilitated by modifications applied to the "ggupdate" processing protocol to streamline database administration steps.


4.Accomplishments
1. Integrating genetic and physical maps with developing genomic sequences. Increasing numbers of small grains genomic and expressed sequence tag (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 this information with grass model systems Brachypodium and rice. ARS scientists in Albany, CA refined and solidified protocols for collecting map data and displaying it in a user-friendly online format that enables comparing maps with each other. Information from model grass species is being staged using computational tools so that comparative views between related grass species are available. The physical map of the wheat relative Aegilops tauschii was integrated with other wheat genetic maps in the GrainGenes resource by use of common markers. A summary table of the wheat maps, and maps of other related grass species is available at http://wheat.pw.usda.gov/ggpages/map_summary.html, and now includes a short list of the most important maps, and it will aid users who are not familiar with the full range of maps available.


6.Technology Transfer

Number of Web Sites Managed7

Review Publications
Anderson, O.D., Gu, Y.Q., Kong, K., Lazo, G.R., Wu, J. 2009. Structure of the omega-gliadin gene family. Functional and Integrative Genomics. 9: 397-410.

Matthews, D.E., Lazo, G.R., Anderson, O.D. 2009. Plant and Crop Databases. In: Somers, D.J., Langridge, P., and Gustafson, J.P., editors. Plant Genomics: Methods and Protocols. New York, NY: Humana Press. P. 243-262.

Last Modified: 12/20/2014
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