Gramene Release 25 June 2007

This release includes:.

Gramene website features:

Gramene Database:

Genomes Release Notes

New Genomes Data

Maps Release Notes

Data in the Maps Module is built out of the mappings in the Markers Module. Updates in the latter module are also reflected here. Of note is the new cytogenetic map of maize from the Cytogenetic Map of Maize project. The gene predictions in the rice genome have been updated to reflect the latest annotations from TIGR release 5.

New maps

Updated gene prediction positions

Updated with new curated QTL

See also the detailed Map Module statistics report.

Markers Release Notes

For release 25, the markers database contains a total of 13,952,872 markers. For the sake of clarity, we have changed the name of the marker type "Gene Model" to "Gene Prediction"; these are genes predicted by TIGR on the rice genome. With the addition of the cytogenetic map of maize, a new marker type "FISH probe" has been added.

Marker breakdown by type

Marker Type Markers
AFLP 8150
Breakpoint interval 303
Centromere 22
Clone 2605818
deletion 895
EST 4661596
EST Cluster 1325127
FISH probe 31
FPC 22651
Gene 9806
Gene Prediction 96234
Gene Primer 19
GSS 4868955
insertion 686
Maize Bin 114
mRNA 142278
OVERGO 25006
Primer 21482
QTL 11437
RAPD 174
RFLP 17744
SSR 14826
SSR Primer Pair 16883
STS 2234
Unclassified DNA 31524
Undefined 68877

Marker breakdown by species

Species Markers
Barley (Hordeum spp.) 682451
Maize (Zea spp.) 4653569
Oat (Avena spp.) 8839
Rice (Oryza spp.) 5124238
Rye (Secale spp.) 13513
Sorghum (Sorghum spp.) 1341868
Sugarcane (Saccharum spp.) 340044
Wheat (Triticum spp. + Aegilops spp.) 1554422
Other 233928

See also the more detailed Marker Module statistics report.

Proteins Release Notes

The Gramene protein database provides curated information on SP-Trembl entries from family Poaceae (Grasses). The annotations include Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO+GRO) and Environment Ontology (EO) are used to provide functional characteristics.

Ontologies Release Notes

Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.

Ontology Total terms    Total Terms w/Associations    Total Associations
Gene Ontology (GO)       24324 3591 454548
Plant Ontology (PO)    828 151 15924
Growth stage Ontology (GRO)    236 90 16081
Trait Ontology (TO)    829 484 13741
Taxonomy Ontology (GR_tax)    2619 1328 180848
Environment Ontology (EO)    497 50 566

Genes and Alleles Release Notes

Content: Number of genes

Improvements include:

A more detailed genes database statistics report can be found here.

QTL Release Notes

The Gramene QTL database now contains a total of 11,437 QTL identified for numerous agronomic traits in rice, maize, barley, oat, wheat, sorghum, pearl millet, foxtail millet and wild rice.

One important improvement in this release is the provision of QTL associated molecular marker info. We currently provide two types of associated markers for a particular QTL: Co-localized markers are the markers co-localized or overlapped with a QTL region on the original QTL map, and neighboring markers are those not overlapped but closely adjacent to a QTL region. The associated marker info is crucial for QTL fine mapping, map-based positional cloning, and marker-assisted selection (MAS) for plant breeding.

Another improvement in this release is the provision of the inferred rice genome positions for recently curated rice QTL. Together with previous QTL genome positions, currently we provide the inferred positions for more than 6,000 rice QTL. These genome positions are displayed on both Gramene Maps and the Genome Browser, and will greatly enhance users' ability to perform comparative mapping research and candidate gene discovery.

Another recent improvement is that all QTL have been described and annotated by multiple ontologies. In addition to Trait Ontology (TO) terms used in previous releases, Plant Ontology (PO) terms have been added to describe Plant Structure and Plant Growth and Development Stage associated with a particular QTL. These terms have been annotated according to the information from QTL experiments in the cited literature, or by creating a default mapping based on the expertly identified TO and PO associations.

A more detailed QTL database statistics report can be found here.

Pathways Release Notes (version 1.3)

RiceCyc is a web based tool for viewing gene annotations mapped to various biochemical pathways in plants: rice (Oryza sativa), Arabidopsis thaliana and bacteria E. coli. This tool also allows you to draw comparisons among the data sets from the above three species.

Sixteen pathways have been deleted and fifteen pathways added during this round of curation. All the pathways changes are recorded here

This tool also allows you to upload your own gene expression data on the pathways to visualise an overview of the cellular level expression profile.
For more information please visit RiceCyc start page.

Diversity Release Notes

The Gramene Genetic Diversity database contains phenotype, SSR and RFLP allelic data for rice, SNP data for Wheat, and phenotypic, SSR and SNP data for maize. Allelic variation on loci of multiple germplasms of a species and genome-wide allelic variation of germplasms can be viewed by searching for locus/marker name, germplasm name or accession number.

On this release:

Click here for database summary.