Location: Genomics and Gene Discovery
2011 Annual Report
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.
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.