Arnis Druka ¹, Ilze Druka ¹, Dave Kudrna ¹, Andris Kleinhofs ²

1 Dept. Crop and Soil Sciences, Washington State University, Pullman, WA 99164

2 Dept. Crop and Soil Sciences and School of Molecular Biosciences, Washington State University, Pullman, WA 99164 e-mail: druka@mail.wsu.edu

Since the construction of the barley BAC library (Yu et al.2000), commencement of several EST sequencing projects (Wing et al. unpublished; Saren et al. 2001; Michalek et al. 2001; Sato et al. 2001) and advancements in barley genetic mapping (Kleinhofs and Graner 1999) the amount of barley genome related information has considerably increased. None of the existing plant databases provides comprehensive, efficient, integrated and user-friendly access to barley genome information. In an attempt to improve the state of barley genomics information, we have started to develop a barley genomics database, which would integrate data from the existing barley genetic and physical maps, mutant information, BAC library screening and EST sequencing and mapping results. The database at this stage of development provides efficient access through a single, web-based interface to the barley genome resources generated in A. Kleinhofs laboratory and gleaned from the published literature. The relevant barley genome information from the other data-sources such as Clemson University Genomics Institute (CUGI) (http://www.genome.clemson.edu), GrainGenes (http://wheat.pw.usda.gov) and IPK Gatersleben (http://pgrc.ipk-gatersleben.de/) are also being integrated.

Important features added are access to the BAC library screening results and EST sequencing data. The DB consists of several cross linked modules, Barley Genetic Marker DB, Barley cv Morex BAC DB, Barley cv Morex EST DB, Barley Mutant DB and Barley Genetic Maps.

Barley Genetic Marker DB (over 2000 records) provides information on mostly RFLP probes, including polymorphism and mapping data, technical characteristics (vector, insert size, etc.), relevant references and RFLP polymorphism images. The features include two search options (simple and complex). Links to the EST and BAC databases are being developed.

Barley BAC DB (10659 individual records, or screening results with 282 probes) contains information on barley cv Morex BAC library screening. The database can be searched against a set of probes and/or BAC addresses. The search results page gives an opportunity to detect overlapping BAC clones. It will be linked to the Barley Genetic Marker DB and EST DB.

Barley EST DB (13967 records) provides access to the barley EST sequences available at Clemson University Genomics Institute (CUGI, http://www.genome.clemson.edu/projects/barley/). Search option allows to find ESTs based on homology hits and ESTs from different cDNA libraries. It has links to Barley Genetic Marker DB, CUGI barley EST sequence depository and GeneBank through the NCBI.

Barley Genetic Maps (SteptoexMorex Bin Maps) at present are available as PDF formatted files (requires Adobe Acrobat Reader) or can be viewed as SVG format files (requires SVG viewer). These formats allow to search for the markers of interest as a text strings and map images can be scaled without image quality loss, thus allowing to display detailed information. Additionally, SVG format allows to add more interactivity to the map images, such as conditional display of genetic and physical map features.

Barley Mutant DB contains data (429 records) published in Barley Genetics Newsletter (BGN) volume 26 (http://wheat.pw.usda.gov/ggpages/bgn/26/). Descriptions and images of mutants maintained in Andris Kleinhofs laboratory are being added to this database. It will be linked to the Barley Genetic Marker DB and to the Integrated Barley Molecular and Morphological/Physiological Marker Maps which are maintained by A. Kleinhofs and published annually in BGN.

Further development of these databases includes addition of current verified data obtained at our lab, as well as data obtained from other scientists. Features will be added and changed according to the needs communicated to us by the users.

The Barley Genome DB is located on Windows NT 4.0 Server operating system running IIS 4 as the http server. This server is a part of a 10 server facility of the College of Agriculture and Home Economics at Washington State University. At present database consists of flat-format modules connected via HTML links. The future technical development will include data transfer to the relational format, most probably to mySQL.

References

Yu Y, J. Tomkins, R. Waugh, D. Frisch, D. Kudrna, A. Kleinhofs, R. Brueggeman, G. Muehlbauer, R. Wise and R. Wing. A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes.TAG 101: 7, pp 1093-1099

Hayes P, A. Castro, A. Corey, L. Marquez-Cedillo, B. Jones, D. Mather, I. Matus, C. Rossi, K. Sato. A summary of published barley QTL reports. http://www.css.orst.edu/cereals/

Kleinhofs, A. and A. Graner, 1999. An integrated map of the barley genome. In: R. L. Phillips and I Vasil, eds., DNA-Based Markers in Plants. Kluwer Acad. Publishers.

Wing, R., Close,T.J., Kleinhofs,A., Wise,R., Begum,D., Frisch ,D., Yu,Y., Anderson,H., Dale,J., Henry,D., Kernodle,S., Palmer,M., Rambo,T., Saski,C., Schwartzbeck,J., Simmons,J., Choi,D.W., Main,D., Wood,T. Development of a genetically and physically anchored EST resource for barley genomics Year: 2000 Status: Unpublished

Ari-Matti Sarén, Jaakko Tanskanen, Alan Schulman. Production of EST tools for barley gene discovery and exploitation. Plant and Animal Genome IX, SanDiego 2001.

Wolfgang Michalek, Ulf Willscher, Andreas Graner, Klaus-Peter Pleissner.B-EST: A barley EST-database. Plant and Animal Genome IX, SanDiego 2001.

Kazuhiro Sato, Daisuke Saisho, Hidekazu Takahashi, Kazuyoshi Takeda. A large scale barley cDNA sequencing program in Okayama University. Plant and Animal Genome IX, SanDiego 2001.