Cold Spring Harbor, NY — Cold Spring Harbor Laboratory researchers Lincoln Stein and Doreen Ware today announce the public release of Gramene version 19. The database provides agricultural researchers and plant breeders with invaluable biological and genomic information about rice and other grasses. Gramene’s web interface facilitates access to genetic and physical maps, sequences, genes, proteins, genetic markers, mutants, QTLs, and published studies, and is used by researchers in more 100 countries. Gramene is a collaborative project between Cold Spring Harbor Laboratory and the Department of Plant Breeding and Genetics at Cornell University.
Rice, maize, sorghum, wheat, barley and the other major cereal crops are mankind’s most important source of calories. Rice is the first crop genome to be fully sequenced and is a model organism for research within the grasses. By using Gramene to explore the rice genome, which is comparatively small, researchers can identify agriculturally important genes in rice and similar genes in maize, wheat, and other grasses.
The name Gramene is based on the Latin, gramen, meaning “grass” and on the Grameen Bank, which makes loans to the rural poor in emerging economies.
New information, features, and tools are continually added to the Gramene database through quarterly releases in January, April, July, and October. Gramene currently hosts the sequenced genome assembly of rice (japonica) and Arabidopsis, as well as a clone-based physical map and partially sequenced genome of maize. For comparative analyses between species, Gramene hosts more than 160 genetic/physical maps from more than 20 cereal species, and several million sequences from more than 60 datasets mapped to the rice genome. A recent addition to the Gramene toolbox is a “Mart” function, which allows researchers to carry out complex searches using an intuitive interface. Online tutorials help users to learn how to search the database.
In addition to offering specific scientific information, Gramene provides information and links of general interest including resources on plant genetics, bioinformatics, and important cereal species. For example, the Oryza (rice) and Zea (maize or corn) species pages have been completed, and other species are under development.
Gramene is a curated, free, web-accessible data resource for comparative genome analysis in the grasses. It is supported by the National Science Foundation and the USDA Agricultural Research Service and was previously funded by the USDA Initiative for Future Agriculture and Food Systems. The database and the curated datasets are also freely available for local use and installation. For more information about Gramene, visit http://www.gramene.org
Founded in 1890, Cold Spring Harbor Laboratory has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. Home to eight Nobel Prize winners, the private, not-for-profit Laboratory employs 1,100 people including 600 scientists, students and technicians. The Meetings & Courses Program annually hosts more than 12,000 scientists. The Laboratory’s education arm also includes an academic publishing house, a graduate school and the DNA Learning Center with programs for middle and high school students and teachers. For more information, visit www.cshl.edu