Gramene: a bird's eye view of cereal genomes

Abstract

Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a compact genome of approximately 400 Mbp, has been sequenced and annotated. The Gramene database (http://www.gramene.org) takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606-1613], the database has undergone extensive changes that are described in this publication.

Figure 1

(A) A flow diagram showing all the modules and datasets (genomes, maps, markers, QTL, genes, proteins, ontologies and literature) present in the Gramene database. Each module connects or links to the information from one to many other modules as depicted by the arrows. The double headed connections suggest that the modules link in both directions. (B) The modified image displayed by the comparative map tool CMap. The CMap tool allows a user to add any number of maps to the left and/or right of the reference map. In this case, the reference map is the sequence map of rice chromosome-3 from the mapset called ‘Gramene TIGR pseudomolecule assembly of IRGSP sequence 2005’. In the first display, the wheat deletion map of chromosome-4D from the mapset ‘Wheat, Physical, EST 2003 (wEST 2003)’ and the maize genetic map of Chromosome-1 from the mapset MMP IBM2 Neighbors 2004 were added to the right and left of the reference map, respectively. The blue colored lines connecting the maps suggest that there is colinearity (conserved synteny) among rice chromosome-3, wheat 4D and maize 1 as demonstrated by the marker order on these maps. Subsequently, a fourth map was added to the display, namely a QTL map of maize chromosome-1 from the map set ‘Iowa Mo17/M99 RI RFLP QTL 1996’. This provided a way to investigate if the maize QTL, GRYLD (for the trait Grain yield, i.e. second from top) contains markers that lead to a colinear region of rice. A comparative map from the maize QTL map to the sequence map of rice enables a user to readily identify putative homologs in the conserved region that may be investigated to determine whether they contribute to the same traits in the two species. The markers highlighted in red on the maize and rice maps are shared marker loci on the different maps. Red colored markers in the CMap display indicate that there is a correspondence between those marker loci and markers present in other maps in the display. The displayed label (symbol) for a QTL represents a trait acronym e.g. GRYLD is for the trait Grain yield.

Figure 2

(A) Rice genome browser. A detail view of a section of rice chromosome-3 where the BAC clone AC119747 is mapped as part of the genome assembly. This genomic clone is the first feature in the view and is described as a DNA contig in blue and labeled with a GenBank accession number. The annotations provided in relation to this BAC represent datasets generated by Gramene using its internal gene prediction pipeline (e.g. Rice_GeneModel-FGENESH) as well as annotations obtained from external databases or individual researchers (as labeled in each track). The views can be customized by the researcher by going to the dropdown menus on the browser views (e.g. Features, ESTs, GSSs, etc.) to display or hide specific tracks, or one can select features in a track by clicking the plus sign next to the track name. A researcher may traverse to a physical map in the comparative map tool by selecting an option from the ‘Jump to’ menu. Genes displayed in grey in the Rice_GeneModel_TIGR track suggest that putative orthologs have been identified in maize and/or Arabidopsis. (B) The detailed view of a gene report page for the gene Loc_Os03g03350 provides a general description of the gene and its functional annotation, as well as specific information about the gene, its introns and exons, the transcript(s), peptide(s), putative orthologs, and also offers a download option.