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December 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 http://www.gramene.org/mailarch-announce/.

To submit items for this newsletter, contact the newsletter editor at: cer17@cornell.edu.

Gramene News:

Come see us at:
Recommended Reading
Gramene FAQ

Community News:

Opportunities
Check out the latest...
Rice Outlook
Community Calendar

Gramene News


Come see us at:
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.
March 15-18, 2007 CSHL Plant Genome meeting
March 22-25, 2007 Maize Genetics Meeting
May 8-12, 2007 Biology of Genomes

Did you know . . .?

Rice Production
2005 Rice Production
In 2005 China and India combined produced over half of the world rice supply. The US ranked 11th for rice production. See Gramene's Species Pages for similar information on other grains.
2005 Rice Production
Rice Production Map 2005

Gramene Release 23!

Gramene is proud to announce the release of Gramene V23. Significant effort has gone into making the database more useful for users. Thank you for your feedback on the database. Please continue to send us your comments - both positive and negative.

In addition to much new and updated data in all the datasets, these changes are outlined in the Release Notes. We recommend that you check out the following significant changes:

Gramene Workshop at PAG XV

Plan now to attend the Gramene Workshop on Tuesday - January 16, 2006, 3:50 pm - 6:00 pm. This workshop is geared for the beginning or intermediate cereal researcher or breeder who may or may not be familiar with Gramene. In this workshop you will get an overview of the Gramene Website, data, and tools, including a formal introduction to the new Diversity and the new Pathways datasets. Learn about the updates to the datasets, including quicker CMap retrieval, Genome browser development, ontology associations, and species Gramene-data summary pages.


 
Recommended Reading from the Gramene Literature Database
  • Genetic Diversity and Origin of Weedy Rice (Oryza sativa f. spontanea) Populations Found in North-eastern China Revealed by Simple Sequence Repeat (SSR) Markers. Cao et al. Annals of Botony (Lond). 2006 Dec;98(6):1241-52. Epub 2006 Oct 20 [PubMed]

  • AgBase: a unified resource for functional analysis in agriculture McCarthy et al. Nucleic Acids Res. 2006; 0:gkl936v1-D5.

  • Comparative Mapping of Growth Habit, Plant Height, and Flowering QTLs in Two Interspecific Families of Leymus. Larson et al. Crop Sci. 2006; 46:2526-2539.

  • Functional Classification, Genomic Organization, Putatively cis-Acting Regulatory Elements, and Relationship to Quantitative Trait Loci, of Sorghum Genes with Rhizome-Enriched Expression. Jang et al. Plant Physiol. 2006; 142:1148-1159.

 
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. In Genomes, where are the SNP from?
A. We display SNPs from two sources; NCBI's dbSNP, which are currently variations between the indica and japonica subspecies reported by BGI, and the OMAP project, which are pseudo-SNPs between O.sativa japonica, and several other closely related Oryza species.
Q. A few months ago the genomes database contain Loc-OS7g26970 and Loc-OS7g26980 but now these two loci are gone. Now you have OS7g26974. Why?
A. For gene names, we take annotations directly from TIGR. When we update to the newest TIGR some gene locii are lost, and others gained. An explanation of TIGRs gene nomenclature can be found here.

Community News



Opportunities:

 
Check out the latest news:

 
US Rice Outlook (From 11/9/06 http://www.usda.gov/oce/commodity/wasde/latest.txt)

U.S. rice production in 2006/07 is forecast at 193.3 million cwt, up 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 6,847 pounds per acre, up 36 pounds per acre from last month, and 211 pounds above 2005/06. Long-grain production is projected at 143.7 million cwt, up 0.8 million cwt from last month, while combined medium- and short- grain production is estimated at 49.6 million cwt, up 0.3 million cwt from a month ago. No changes are made on the use side. Exports are projected at 97 million cwt. Ending stocks of all rice are projected at 34.5 million cwt, 1.0 million cwt above last month but 8.5 million below a year earlier. The season-average farm price is projected at $9.00 to $9.50 per cwt, unchanged from last month.

Global 2006/07 rice production and consumption are lowered from a month ago, while trade and ending stocks are little changed. Global production is projected at 416.5 million tons, 0.9 million tons below last month, but 1.0 million tons above 2005/06. The decrease in global production is due primarily to smaller crops projected for Brazil, Burma, and Thailand. Brazil's 2006/07 production is projected at 7.9 million tons, 600,000 tons below a month ago due to a decrease in area. Global rice ending stocks for 2006/07 are projected at 78.8 million tons, down slightly from last month but down 1.7 million tons from 2005/06.
For more indepth information, see:

 Upcoming Meetings
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.
February 7-9, 2007. National Plant Breeding Workshop. Raleigh, NC, USA
March 15-18, 2007 CSHL Plant Genome meeting
March 22-25, 2007 Maize Genetics Meeting
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.
May 8-12, 2007 Biology of Genomes
May 31- June 3, 2007. 9th Annual Plant Sciences Institute Symposium on Epistasis: Predicting Phenotypes and Evolutionary Trajectories. Ames, Iowa, USA.
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
August 11-15, 2008. The Fourth International Conference on The Comparative Biology of the Monocotyledons & The Fifth International Symposium on Grass Systematics and Evolution. Copenhagen, Denmark
See also: