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United States Department of Agriculture

Agricultural Research Service

Research Project: Small Grains Database and Bioinformatics Resources

Location: Genomics and Gene Discovery

2013 Annual Report

1a.Objectives (from AD-416):
Over the next 5 years the project will focus on the following specific objectives as part of the long-term purpose to synthesize, display, and provide access to small grains genomics and genetics data for the research community and applied users.

Objective 1: Annotate wheat, barley and oat whole genome sequences in collaboration with the crop research communities and integrate with genetic, physical, and trait maps. • Sub-objective 1.A. - Contribute to wheat gennome annotations and incoporation of small grains annotations into GrainGenes. • Sub-objective 1.B. - Collaborate in integrating small grains genetic, physical, and trait maps. • Sub-objective 1.C. - Modifying GrainGenes with enhanced user tools in accessing genomic and mapping data.

Objective 2: Integrate genotyping and phenotyping results from the Triticeae Coordinated Agricultural Project (T-CAP) including the T3 database, the National Small Grains Collection and GRIN database, and Gramene, to enhance support for trait analysis by association mapping and trait improvement by genomic selection. • Sub-objective 2.A. - Collaborate in developing common standards describing phenotypes and traits across species. • Sub-objective 2.B. - Convert data from GRIN, ARS Genotyping Laboratories, and the small grains Regional Field Nurseries to GrainGenes database formats. • Sub-objective 2.C. – Modify the GrainGenes schema to accommodate increased data volume and utilization.

Objective 3: Collate, analyze, and present trait data from wheat, barley and oat communities to facilitate the genetic improvement of target traits and trait gene isolation. • Sub-objective 3.A. - Collate data on target traits. • Sub-objective 3.B. - Implement tools and interfaces for map displays.

Objective 4: Maintain existing and develop new user community outreach. • Sub-objective 4.A. - Solicitation of user community input. • Sub-objective 4.B. - Training and education for use of GrainGenes resources.

1b.Approach (from AD-416):
1) Contribute to the annotation of whole genome sequences of wheat, barley, and oats in collaboration with the research community along with other national and international small grains genomics efforts.

2) Incorporation of genomic sequences and maps (genetic, physical, trait) into GrainGenes. To include integration of maps from multiple sources and related data sets already represented within GrainGenes.

3) Integrate genotyping and phenotyping data into GrainGenes. To include collaborating the GRIN, Gramene, and the Triticeae T-CAP project.

4) Modify the GrainGenes web site with enhanced user tools for accessing data, implement tools and interfaces for enhanced map displays, and modify the GrainGenes database schema to accommodate larger data sets. To include a complete rewrite and redeign of the GrainGenes web site and databases.

5) Enhanced research community outreach through regular solicitation of user community input, development of social medium tools for data access and user training, and develop formal training manuals and training manuals for GrainGenes users.

3.Progress Report:
This is a new project which continues the research from 5325-21000-014-00D, "An Integrated Database and Bioinformatics Resource for Small Grains." Please see the report for 5325-21000-014-00D for more information.

Last Modified: 4/18/2014
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