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United States Department of Agriculture

Agricultural Research Service

Research Project: AN INTEGRATED DATABASE AND BIOINFORMATICS RESOURCE FOR SMALL GRAINS
2011 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.


3.Progress Report
With wheat genome sequencing increasing on the research front, curator processing of small grains research information allowed genetic and physical maps to be integrated into GrainGenes. From the wheat capacity project (CAP), molecular markers yielded maps related to phenotypic traits for disease resistance and grain quality, allowing GrainGenes to document its progress before it initiates a new phase of research associated with the newly formed Triticeae CAP. Similarly, integrated maps of barley were placed on GrainGenes from population studies. Final maps summarizing the barley CAP were also loaded as it has now joined the efforts supporting the Triticeae CAP project.

Collaborations with the oat community yielded the first major advance in oat expressed sequence tags and assisted in the design of single-nucleotide-polymorphism (SNP) probes for the differenting oat germplasm. Probe design and screening serves as first steps in establishing a marker-assisted selection system for association mapping studies to improve key traits in oat; mapping studies are now underway in North America and are expanding to be a global effort. Collaborations to generate maps with groups working on forage grasses were also initiated, and preliminary maps are in preparation before publication. Comparative maps allowed collaborators to focus on key traits and attributes that can be applied to a wide range of studies including crop improvement, bioenergy, and range ecology; these and other findings may lead us to a better understanding of the diversity in form and function of the grass species.

Major progress was made toward transferring The Hordeum Toolbox (THT) to the GrainGenes project as the barley CAP closed. The importance of using molecular markers to track phenotypic and genotypic data for agronomic and plant quality traits in breeding lines was a capital point in this study, and is being carried forward with the combined wheat and barley CAP projects know as the Triticeae CAP (TCAP). Collaborations with programming developers continues to improve data tool development. Enhancements have been made toward importing/exporting data, specialized curation tools, and display of genotyping data. Software improvements have occurred under the GrainGenes, THT, and T3 databases. The feasibility for using expanded genome and data software were also tested as a platform to view data in a different perspective.

The website for the US Wheat and Barley Scab Initiative, www.scabusa.org, was enhanced with additional features and redesign. The “FHB Alerts” regions were reconfigured and an administrative interface was created to manage the FHB Alert subscriptions; these updates were advertised by poster at a recent barley conference. Web site forms and server-side processing scripts used for authorized credit processing, database registration and procedure ordering, a tool vital towards organizing project activities, was updated. The USWBSI server was updated, and the scabsmart.org web-site was integrated into this resource.


4.Accomplishments
1. Integrating genetic and physical maps with developing genomic sequences. The combination of additional genome sequence resources and the improvements in computer technology have led to improved ways for the researcher to access information. Efficient access to maps of small grains crop genomes is critical to grain crop improvement. Several species of the Triticeae, mainly wheat and barley, and some of the related species are actively being sequenced and studied. Progress made within the GrainGenes project have aided in providing data in a user-friendly way. GrainGenes continues to serve the research community in providing resources to deposit and analyze data, and to develop a platform to provide the data to the public. A wealth of genetic maps and accompanying data are currently available for wheat, barley, oat and grass species and for forming the foundation for discoveries for the GrainGenes-associated species.


Review Publications
You, F., Huo, N., Deal, K., Gu, Y.Q., Luo, M., Mcguire, P., Dvorak, J., Anderson, O.D. 2011. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. Biomed Central (BMC) Genomics. 12:59.

Oliver, R.E., Lazo, G.R., Lutz, J.D., Rubenfield, M.J., Tinker, N.A., Anderson, J.M., Wisniewski-Morehead, N.H., Adhikary, D., Jellen, E.N., Maughan, P.J., Brown Guedira, G.L., Chao, S., Beattie, A.D., Carson, M.L., Rines, H.W., Obert, D.E., Bonman, J.M., Jackson, E.W. 2011. Model SNP development based on the complex oat genome using high-throughput 454 sequencing technology. Biomed Central (BMC) Genomics. 12:77.

Last Modified: 12/21/2014
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