GRAINGENES REPORT

V.L. Carollo¹, D.E. Matthews², G.R. Lazo¹, O.A. Anderson¹
Agricultural Research Service - USDA
¹Western Regional Research Center, Albany, CA
²Cornell University, Department of Plant Breeding, Ithaca, NY

    GrainGenes, the Triticeae genome database (http://wheat.pw.usda.gov), is the most comprehensive source of information on barley, wheat, rye and oats. GrainGenes is maintained at the USDA/ARS/WRRC in Albany, CA and is a central repository for information on gene and expressed sequence tag (EST) sequences, genetic and physical maps, DNA probes, germplasm, pathology, and other data types. GrainGenes may also be accessed through a mirror sites at INRA, France (grain.jouy.inra.fr) and NRC-PBI, Saskatoon, Canada (gene.pbi.nrc.ca/graingenes/).

    Sequencing efforts have yielded an enormous wealth of data for Triticeae genomics in the last few years. Currently GrainGenes holds records for over 150,000 barley gene EST sequences. Although these sequences are deposited in GenBank and are available to the public, further efforts by the GrainGenes curators have improved the accessibility and added information, such as map location when available. Sequence records in GrainGenes are linked to external databases including the NCBI UniGene clusters (www.ncbi.nlm.nih.gov/UniGene/), TIGR Gene Indices (www.tigr.org/tdb/tgi/) and homologous sequences in the rice genome from Gramene (www.gramene.org/).

    The number of interactive maps - with each locus linked to documentation about its probe or gene - from published genetic and physical map projects distinguishes GrainGenes as an important research tool. Currently there are 31 sets of Hordeum maps in the database (See Table 1). Recent additions to the map collection include the updated linkage map of the Oregon Wolfe Barley (OWB) population, which is accompanied by 38 image files of the OWB naked-eye phenotypes (NEPs) (Wolfe, et al. 1996), and two map sets with SSR markers (Ramsay, et al. 2000; Pillen K, et al. 2000). GrainGenes curators constantly monitor the literature for new maps to add to the collections. These planned additions can be viewed at the Mapathon web page (wheat.pw.usda.gov/ggpages/ggmapathon.html).

    Another new addition to the GrainGenes map collection is the barley bin maps from Washington State University, which include markers from several map studies. This map is available via Gbrowser, a new map-viewing tool developed by the Generic Model Organism Database Project that has been implemented on GrainGenes. An attractive feature of the Gbrowse viewer is the ability to perform third party annotation. Users can upload preliminary data such as new markers or transposon insertion sites to the maps and then store the new maps privately on the GrainGenes server for later additions, edits or deletions. When the user returns to the map viewing web page, the software recognizes the users computer via "cookies" to enable viewing and editing the customized maps. Users can also create web pages from the new maps to share with collaborators. A link to this tool is available via the "Maps and Map Data" web page (wheat.pw.usda.gov/ggpages/maps).

    GrainGenes curators have worked with curators at Gramene (www.gramene.org) and NCBI (www.ncbi.nlm.nih.gov) to provide data and link to comparative mapping tools for barley. The Gramene project compares genomes across species. Users can align the North American Barley Genome Mapping Project (NABGMP) Steptoe x Morex maps with selected maps from rice, wheat, oat, maize and sorghum. Another new comparative mapping tool is available at the Plant Genomes Central, a new site at NCBI dedicated to plant genomics (www.ncbi.nlm.nih.gov/PMGifs/Genomes/PlantList.html). Barley maps can be compared to each other and include two consensus maps (Langridge, et al. 1995; Qi, et al. 1996), the NABGMP Steptoe x Morex (Kleinhofs, et al. 1993) and Harrington x TR306 (Kleinhofs A. personal communication).

    Data from mapping populations are also available on the website and include raw data, QTL scans, linkage maps as line drawings and phenotypic data. Two recent additions from Hayes et al. (personal communication) include Harrington x Morex (wheat.pw.usda.gov/ggpages/HxM) and Shyri x Galena (wheat.pw.usda.gov/ggpages/SxG) Other new genomic tools for barley research are available via GrainGenes. TREP, the Triticeae Repeat Sequence Database (wheat.pw.usda.gov/ITMI/Repeats/), curated by Thomas Wicker (Institute for Plant Biology, Zurich Switzerland), is an annotated, BLASTable collection of repetitive DNA sequences retrotransposons, transposons, foldback elements, and tandem repeats. The Triticeae EST-SSR Coordination project (wheat.pw.usda.gov/ggpages/ITMI/2002/EST-SSR) organized by Nils Stein (IPK, Gatersleben, Germany) compiles microsatellite-containing ESTs from the Triticeae that are organized in "superclusters" by sequence similarity, as well as SSRs in known barley genes.

    Although the majority of new information on GrainGenes is derived from genomics projects, the GrainGenes curators strive to offer the most complete and up to date information on other topics important to Triticeae researchers. GrainGenes holds information on Hordeum germplasm with 582 germplasm and 175 species records online. GrainGenes also contains information on pathology with 147 records, many of them with images of the causal organism or disease symptoms. New additions to GrainGenes, including new maps, are reported in the "What's New" page on the project homepage. An open invitation is extended to the research community to suggest improvements and contribute data for this public database.

References

Kleinhofs A, et al. (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor. Appl. Gen. 86:705-712.
Langridge P, Karakousis A, Collins N, Kretschmer J, Manning S (1995) A consensus linkage map of barley. Mol. Br. 1:389-395.
Pillen K, et al. (2000) Mapping new EMBL-derived barley microsatellites and their use in differentiating German barley cultivars. Theor. Appl. Genet. 101:652
Qi X, Stam P, Lindhout P (1996) Comparison and integration of four barley genetic maps. Genome. 39:379-394.
Ramsay L, et al. (2000) A simple sequence repeat-based linkage map of barley. Genetics 156:1997.
Wolfe RI, Hayes PM, Shugar L (1996) Multiple dominant and recessive genetic marker stock development. BGN 25:18.