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November 2006 Newsletter

Gramene is updated four times a year. To receive email notification of updates to the Gramene website, you may join the Gramene-announce listserve at

To submit items for this newsletter, contact the newsletter editor at:

Gramene News:

Upcoming Gramene Activities
Recommended Reading
Gramene FAQ

Community News:

Check out the latest...
Rice Outlook
Community Calendar

Gramene News

Come see us at:
November 8-11, 2006 Crop Genomics, Trait Analysis and Breeding, Hinxton, UK.
  • The Gramene Genome Browser; Visualisation of Annotation on Plant Genomes
December 4-6, 2006 Data Warehouse Technologies in Bioinformatics, Leucorea, Wittenberg, Germany.
  • Gramene: a community resource for plant comparative genomics
January 13-17, 2007 Plant and Animal Genome XV Conference, San Diego, CA, USA.
  • Gramene demo/workshop
  • Posters on Gramene Updates, Biochemical Pathways, Genetic Diversity, Ontologies, and the Species pages.

Did you know . . .?

Cereal consumption
5-year Average (1999-2003)
In 2004, the global average consumption of cereals was 1188 calories/day. Rice, maize and wheat have the higest consumption (and therefore production) of the cereals. For more information on cereal production and consumption, see Gramene's Species Pages
2005 Rice Production
Rice Production Map 2005

The 2006 Nobel Peace Prize

The 2006 Nobel Peace Prize was awarded to Muhammad Yunus and the Grameen Bank "for their efforts to create economic and social development from below" [see Nobel for anti-poverty pioneers.] In 1976 Professor Yunus initiated the Grameen Bank Project with a plan to improve the lives of rural poor through microcredit for establishing businesses. In 1983 Gramene Bank became an independent bank, and is currently 90% owned by the rural poor whom it serves. 97%of the 6.67 million borrowers are women. Yunus's long-term vision is to eliminate poverty in the world, a goal for which micro-credit is one tool. For more information about the Grameen Bank, visit

Here at the Gramene database we are delighted to recognize this honor to Muhammad Yunus and Grameen Bank. Although there is no official connection between Grameen Bank and Gramene database, Gramene adopted our name as a play on the term "Grameen", which means "rural", and on the similarity of our goals. The Grameen bank in Bangladesh - where coincidently the average person in 2003 received 1600 of their 2100 daily calories from rice - has a mission to serve the poorest of the poor, and to improve lives. Similarly, the data in Gramene has the potential to be used to improve lives. In order to meet the demand for food in a world that is exploding in population and loosing cropland, it is essential that we develop new strains of crops that have expanded ranges, shortened growing seasons, increased resistance to pests and other environmental stresses, enhanced nutritional value and other beneficial agronomic characteristics. Genomic research provides the foundation for this.

Cereals are a staple food source for all people. For example, cereals supply 1800 calories a day in Burkina Faso, 1600 calories per day in Mali, and 1500 calories per day in Niger. But, especially in the world's poorest countries, a single cereal may serve as the staple food in the poorest countries of the world, such as rice in Myanmar (1900 calories) and Viet Nam (1600 calories), maize in Lesotho (1500 calories) and Malawi (1100 calories), and millet in Niger (1050 calories). Even the United States and western European countries rely on grain to directly provide over 800 calories a day, while grains and grass forages feed the livestock which provide another significant portion of daily nutrition.

The origins of Gramene were in a database called RiceGenes. With the smallest genome of the cereals, rice serves as a model organism for research in the other grasses – grains and forage grasses. It is through databases such as RiceGenes where the accumulated global knowledge is stored and made accessible to breeders and researchers, who work to improve cereal production and nutritional quality.

The natural growth of RiceGenes into a database for many of the grasses called for a name that encompassed all of the grains. The grass family is called "Poaceae" or "Graminae", and the similarity between Graminae and Grameen was striking. With a play on words, Gramene was born.

Recommended Reading from the Gramene Literature Database
  • Ren et al. In plants, highly expressed genes are the least compact. Trends in Genetics, 2006, 22: 528-532. [More Info]

  • Rehmeyer, et al. Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae. Nucl. Acids Res. 2006. 34: 4685-4701.

  • Buckler et al. Molecular and functional diversity of maize. Current Opinion in Plant Biology. April 2006, 9(2): 172-176. [More Info]

Gramene FAQ. Gramene users are encouraged to contact Gramene for assistance in using the database. In addition to attending workshops, users contact Gramene through the "Feedback" link at the top of any page, or join the Gramene listserve.
Q. Recently I was pointed to Gramene as a successful example of a biological database. I did not find a description of the data model on your website. Is this information available?
A. Gramene's data model has developed rather organically over the years as a result of how we've absorbed various legacy databases (RiceGenes) or developed novel tools (CMap) or incorporated/customized third-party software (Ensembl, EcoCyc, GO) or taken on new datasets (proteins, genes). As such, we really have many fairly distinct "modules" that can be curated independently and which join up through a set of conventions, cross-references, and ontologies. You can go to our FTP site to examine our schemas and get the MySQL dumps of all our databases. Or you can download the latest tarball of our software distribution and inspect the Class::DBI classes we generate from them in the "lib/perl/Gramene/CDBI" directory. The raw schemas are not part of our tarball, which is something I was considering adding for the next release. Keep in mind the number of non-Gramene tools we use, too, when trying to get an idea of all our pieces. You'll have to go get CMap (available at the GMOD Sourceforge site or our FTP), the Ensembl code (see the "README.ensembl" file in our tarball), the Gene Ontology schema (also a SF project), etc.

Community News


Check out the latest news:

US Rice Outlook (From 10/12/06

U.S. rice production in 2006/07 is forecast at 192.3 million cwt, down about 1.0 million cwt from last month. Harvested area remains projected at 2.82 million acres, down 16 percent from a year earlier. The average yield is estimated at 6,811 pounds per acre, down 35 pounds per acre from last month. Long-grain production is projected at 142.9 million cwt, 0.7 million cwt below last month, while combined medium- and short-grain production is estimated at 49.4 million cwt, down 0.3 million cwt. Imports are forecast at a record 18 million cwt, up 0.5 million cwt from revised 2005/06. Domestic and residual use is forecast at 122.8 million cwt, down 2.1 million cwt from last month, but up 3.6 million cwt from revised 2005/06. Total exports are unchanged at 97 million cwt; however, rough rice exports are lowered 2 million cwt to 35 million cwt and combined exports of milled and brown rice are raised 2 million cwt to 62 million cwt (on a rough-equivalent basis). Long- grain exports are lowered 1 million cwt to 75 million cwt, while combined medium- and short-grain exports are raised 1 million cwt to 22 million cwt. Ending stocks of all rice are projected at 33.4 million cwt, 1.6 million cwt above last month. The season-average farm price is projected at $9.00 to $9.50 per cwt, up $0.25 per cwt on each end of the range compared to last month.

Global 2006/07 rice supply and use are little changed from a month ago. World production is lowered slightly primarily because of a decline in Australia (-0.5 million tons), which is nearly offset by an increase for Pakistan (0.4 million tons). Ending stocks are lowered 0.6 million tons from last month to 78.8 million tons due mainly to reductions for China, EU-25, and Egypt.
For more indepth information, see:

 Upcoming Meetings
November 8-11, 2006. Crop Genomics, Trait Analysis and Breeding. Hinxton, UK
December 4-6, 2006. Data Warehouse Technologies in Bioinformatics. Leucorea, Wittenberg, Germany
December 9-13, 2006. ASCB 46th Annual Meeting
Dec 15-17, 2006. International Symposium on Computational Biology & Bioinformatics (ISBB), Bhubaneshwar, India
January 3-7, 2007. Pacific Symposium on Biocomputing, Wailea, Maui.
January 11, 2007. Conference in Systems Biology, Bioinformatics and Synthetic Biology. Manchester, UK.
January 13-17, 2007. Plant and Animal Genome XV Conference
January 21-24, 2007. 5th European Conference on Computational Biology, Israel.
January 25-27, 2007. Genis International Conference 2007: "Governing Genomics - Interdisciplinary Perspectives on the Regulation of the Biosciences. University of Exeter, UK.
February 1-2, 2007. Beneath the Hull: Exploiting the Health-Beneficial properties of the Rice Grain. New Orleans. A rice utilization workshop.
March 23-27, 2007. 2nd International Conference on Plant Molecular Breeding. Sanya City, Hainan, P. R. China. This event will focus on Applied plant genomics and molecular plant breeding in view of the increasing need to use newl molecular approaches and mine novel gene resources. All important aspects of plant molecular breeding and related transgenic ecological risk and intellectual property right (IPR) will be covered in several sessions and satellite workshops.
April 11-13, 2007.5th European Conference on Evolutionary Computation Machine Learning and Data Mining in Bioinformatics. Valencia, Spain.
July 21-25, 2007. 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB). Vienna, Austria: July 21-25, 2007
August 13-17, 2007. Computational Systems Bioinformatics, UC San Diego.
January 12-16, 2008. PAG-XVI
See also: