By Jeannie Griffith

Susan McCouch’s 1990 doctoral thesis presented the first molecular linkage map of the rice genome. This impressive accomplishment, which she undertook as a student of Steven Tanksley, the Liberty Hyde Bailey Professor of Plant Breeding and Genetics, laid the foundation for the 14-year-long international effort to map and finally sequence the entire rice genome. McCouch — who is now a professor of plant breeding and genetics with joint appointments in Plant Biology and International Programs — played an important role, along with other members of her laboratory, in bringing the map to completion two years ago.

But McCouch and her colleagues have done something else to advance the knowledge of the international plant genetics/genomics community. A database, RiceGenes, which graduate student Edyth Paul initiated in the McCouch laboratory in 1993, has evolved into a major worldwide resource called the Gramene database (www.gramene.org) that is providing the organizational framework for comparative genome analysis and genetic, physical, and sequence mapping of all the major grass species, including rice, maize, sorghum, sugarcane, wheat, barley, oat, and rye.

A curated, free-for-use, web-accessible data resource, Gramene is a collaborative effort between the Department of Plant Breeding and Genetics (http://plbrgen.cals.cornell.edu/), Cold Spring Harbor Laboratory (www.cshl.edu), and various national and international projects dedicated to cereal genomics and genetics research. McCouch and co-investigators Edward S. Buckler, USDA-ARS and Cornell University, and Pankaj Jaiswal, Department of Plant Breeding and Genetics, have responsibility for releasing quarterly upgrades in collaboration with co-investigators Lincoln Stein and Doreen Ware of Cold Spring Harbor Lab. Their work is supported by grants from the National Science Foundation, the USDA Initiative for Future Agriculture and Food Systems, and a USDA-Agricultural Research Service specific cooperative agreement.

As the first crop genome to be fully sequenced, the rice genome has provided very valuable insight into the structure and function of other crop-grass genomes. Large segments of the rice genome have been found to match very closely the gene order of maize, sorghum, barley, wheat, rye, sugarcane, and other crop grasses. Gramene's web interface provides information on genetic and physical maps, sequences, genes, proteins, genetic markers, mutants, quantitative trait loci, phenotypes, germplasm, diversity, publications, and controlled vocabularies to researchers in over 100 countries around the world. The accessibility of this information should greatly speed the isolation and characterization of genes of interest in all grass species.

Gramene hosts the two sequenced genome assemblies of rice (Rice-japonica, cv Nipponbare and Rice-indica, cv 9311) as well as Arabidopsis and the clone-based map of maize, and provides alignments of expressed sequence tags (ESTs) from all the grasses along the rice genome. GrameneMart, a recent addition to the Gramene toolbox, is a search tool that allows researchers to conduct complex searches using an intuitive interface. Online tutorials help users learn how to search the database.

Gramene also offers information and links of interest to the general student, including resources on genetic research, bioinformatics, and cereal species. The Oryza (rice) and Zea (maize or corn) species pages have been completed, and other species are under development.

Cereal crops are mankind’s most important source of calories. Understanding their genetics is the key to improving the yields, environmental adaptation, and nutritional content of these crops — which is critical to improving the food security of millions of people.