Gramene, a Tool for Grass Genomics

Abstract

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database, providing seamless connections between independent sources of information. Genetic, physical, and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa) are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using gene ontology terms that have been adopted by numerous model species databases. Genetic variants including phenotypes are annotated using plant ontology terms common to all plants and trait ontology terms that are specific to rice. In this paper, we present a brief overview of the search tools available to the plant research community in Gramene.

Genetic control of branching in foxtail millet

“…In some cases, gaps between common markers were larger than the 1-LOD confidence intervals of the QTL, but estimates of QTL positions were done as precisely as possible. MAIZEGDB (24) and GRAMENE (25,26) were used to identify genes that had mutant phenotypes in which vegetative branching was affected. These genes were then located on the foxtail millet map by means of the common markers.…”

Theindeterminate gametophyte1Gene of Maize Encodes a LOB Domain Protein Required for Embryo Sac and Leaf Development

“…Fine mapping of ig1 against available simple sequence repeat markers placed ig1 between umc1311 and umc1973 on chromosome 3 of maize. The rice orthologs of the markers around ig1 were identified by BLAST search for each sequence against the rice genome using the Gramene database for comparative grass genomics (www.gramene.org) (Ware et al, 2002). The orthologs of umc1311 and umc1973 on rice chromosome 1 are ;845 kb apart (Figure 2).…”

Identification and Characterization of Regions of the Rice Genome Associated With Broad-Spectrum, Quantitative Disease Resistance

“…Finally, the relationships of applied using the program IDEG6 (Romualdi et al 2003), genes and EST libraries were evaluated on the basis of their correcting for multiple tests by the Bonferroni (␣ ϭ 0.05) and digital Northern patterns using complete linkage hierarchical false discovery rate (q* ϭ 0.05; Benjamini and Hochberg clustering (Euclidean distance) with the program Genesis 1995) methods. (Sturn et al 2002).…”

“…Cluster analysis was used to group genes (Sturn et al 2002) on the basis of their digital Northern profiles. QTL).…”