Gramene Newsletter Gramene News ArchivePast and Upcoming Outreach


July 2006 Newsletter



Gramene at RiceCAPs
On June 8th Gramene presented a hands-on workshop to students at the 2006 RiceCAP workshop “DNA Markers, Mapping, And Beyond." Attendees learned about some of the basics of searching scientific databases and the importance of using the right search term. During the lab students found literature on "milling yield", searched QTL related to this trait, and identified corresponding markers for those QTL. Forward and reverse primers, as well as annealing temperature and PCR images, were identified for these markers. In addition, the Diversity and Pathways modules were introduced, helping researchers to use these new resources to compare germplasms and search biochemical pathways.

The Gramene database continues to grow and add new features, so helping users to keep up-to-date on the search capabilities of the datasets is key to their efficiency in data identification. Researcher input is essential to improving the user interface of Gramene and other scientific databases, and these workshops continue to offer the opportunity for users to ask questions and provide direct feedback to the Gramene developers. Our workshop materials from RiceCAP are now available online.

Visit with Gramene at

The deadline for submission to Rice Genetics Newsletter Vol. 23 is July 10th. http://www.shigen.nig.ac.jp/rice/oryzabase/rgn/newsletter.jsp

Recommended Reading
  • A silicon transporter in rice. Ma et. al. Nature, 2006, 440, pp.688-691 (More info).
  • An SNP Caused Loss of Seed Shattering During Rice Domestication. Konishi et al. Science, 2006. (More info).
  • Rice domestication by reducing shattering. Li et al. Science , 2006, 311, pp.1936-1939. (More info).
  • Ethanol can contribute to energy and environmental goals. Farrell et al. Science , 2006, 311, pp.506-508. (More info).
  • How fast was wild wheat domesticated? Tanno & Willcox. Science , 2006, 311, pp.1886-1886. (More info).
  • A trehalose metabolic enzyme controls inflorescence architecture in maize. Satoh-Nagasawa et al. Nature , 2006, 441, pp.227-230. (More info).

  • 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. Here are some recent questions that have been added to Gramene's FAQ's.
    Q - I use TblastX to search for homology of my sequences. How can I determine the minimum score to consider as significant for classification?

    A - You can use the 'configure' option of the BlastView interface to set the tblastx parameters to any that you want. We cannot suggest any minimum score as such, as this will depend on many factors specific to your sequences. A good reference on the subject is Korf et.al.'s O'Reilly book on Blast - www.oreilly.com/catalog/blast/
    Q - I tried installing the latest version of Gramene (21), but the 'Apache' perl module tries to install mod_perl 1.99, which only works with Apache 1.3.x. I use Apache 2.x.

    A- Gramene is incompatible with Apache 2 and will only work with Apache 1.3.x. However, you can just compile a 1.3.x version into something like "/opt/apache1/" and have it listen on an alternate port (say "81"?). You can seamlessly proxy all Gramene-related requests through your Apache 2 server to this alternate server.

    Check out the latest Texas Rice Crop survey.

    Dr. Susan McCouch, Gramene PI, presents on DNA at local highschools. Read the article here.



    US Rice Outlook (From 6/9/06 http://www.usda.gov/oce/commodity/wasde/latest.txt)

    No changes are made to the U.S. rice supply and use projections for 2005/06 and 2006/07. However, the season-average farm price range for 2005/06 is narrowed $0.05 per cwt on each end to $7.65 to $7.75 per cwt; and the season-average farm price for 2006/07 is unchanged at $9.00 to $9.50 per cwt.

    Global 2006/07 rice production and consumption are increased from last month while ending stocks are lowered. Global 2006/07 rice production is projected at a record 417.5 million tons, up 0.5 million from last month. The increase in production is due primarily to larger crops projected for India (+1.0 million tons), Nepal, the Philippines, and Iran; which is partially offset by a reduction > for China (-1.0 million tons). World consumption is projected at a record 424.8 million tons, up 1.6 million tons from last month. Ending stocks are projected at 60 million tons, down nearly 2 million tons from last month. The 2005/06 production estimate for China is lowered 1 million tons to 126.4 million tons based on official data from the government of China.
    For more indepth information, see:

    Upcoming Meetings
    June 29, 2006. The LSU AgCenter Rice Research Station's Annual Field Day. Field tours will begin at 7:30 am with the last tour departing the drier at approximately 9:15 am. The poster session will be held under the equipment shed next to the drier from 7:30-10:30 am. The main session will begin in the drier at 10:45 am and the field day will conclude with a sponsored lunch.
    July 6, 2006. 2006 Cornell Seed Growers Field Day NYSIP Foundation Seed Barn, 791 Dryden Road, Rt. 366, Ithaca, NY
    July 16-21, 2006. Plant Molecular Biology Gordon Conference, in New Hampshire, traditionally covering a wide range of topics: plant-microbe interactions, development, metabolism, epigenetics and hormones, using approaches ranging from cell biology and biochemistry to genetics and genomics.
    August 5-9, 2006. Joint Annual Meeting of the American Society of Plant Biologists and the Canadian Society of Plant Physiologists Société Canadienne de Physiologie Végétale. Hynes Convention Center, Boston, Massachusetts. The American Society of Plant Biologists was founded in 1924 to promote the growth and development of plant biology, to encourage and publish research in plant biology, and to promote the interests and growth of plant scientists in general. Over the decades the Society has evolved and expanded to provide a forum for molecular and cellular biology as well as to serve the basic interests of plant science. It publishes the highly cited and respected journals Plant Physiology and The Plant Cell. Membership spans six continents, and our members work in such diverse areas as academia, government laboratories, and industrial and commercial environments. The Society also has a large student membership. ASPB plays a key role in uniting the international plant science disciplines.
    August 6-10, 2006. ISMB 2006. Intelligent Systems for Molecular Biology (ISMB) is the annual meeting of the International Society for Computational Biology (ISCB). Over the past twelve years, the ISMB conference has grown to become the largest bioinformatics conference in the world. The ISMB conferences provide a multidisciplinary forum for disseminating the latest developments in bioinformatics. ISMB brings together scientists from computer science, molecular biology, mathematics, and statistics. Its principal focus is on the development and application of advanced computational methods for biological problems.
    October 9-11, 2006. The 4th International Rice Functional Genomic Symposium will be held in Montpellier, France. This unformal consortium was created in 2000 with a goal to orientate, organise and coordinate rice functional genomic research worldwide and to share a number of resources created in various labs and countries (http://www.iris.irri.org/IRFGC/). An important purpose of this annual symposium is to focus on most recent results and to promote interactions between participants in an informal and friendly atmosphere.
    January 13-17, 2007. Plant and Animal Genome XV Conference
    January 12-16, 2008. PAG-XVI
    See also: Cold Spring Harbor Laboratory - Meetings and Courses