December 2006 Newsletter

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

• In Genomes: Check out the tree-based visualisation of orthologs/paralogs for rice/maize/arabidopsis.
  
• In Maps, notice that the speed of rendering maps has increased. You will find fewer features in the CMap viewer, because only significant features were imported into CMap. To view all features on a map, please refer to the Markers DB Map Sets, or the Genome Browser
• In order to enhance the integration of all the datasets, you may notice that ontology associations are continuing to be built with genes, gene models, proteins, QTLs, markers and maps.

• 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.

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.

• Assistant/Associate Professor (Wetland Plants Breeder/Ecologist) Department of Agronomy and Environmental Management, LSU Agricultural Center, Baton Rouge, Louisiana.
  
  Full-time, 12-month, tenure-track position as part of the LSU Agricultural Center's Coastal Plants Improvement Program. The scientist in this position is expected to develop a creative, productive and competitive research program that applies plant breeding methods to native Louisiana coastal wetlands species in order to enhance their usefulness in coastal preservation and conservation activities. This person will work with other scientists to identify, develop and evaluate genetic and breeding populations of diverse wetland species for use in coastal stabilization and wetlands reclamation. Members of the research faculty are expected to secure extramural funding, publish in refereed journals, and direct graduate student research programs, as a member of the Louisiana State University graduate faculty.
  
  Qualifications: Ph.D. in Plant Breeding/Genetics/Ecology or related field. Training and/or experience in management of plant eco-systems, and knowledge of the use of molecular markers and related techniques in plant breeding is desirable. Strong organizational, written and verbal communication skills are required. The ability to work in a team environment is essential.
  
  If interested, call Dr. Freddie Martin (225-578-2110) as soon as possible
  
  
• Professor/Associate Professor/Senior Lecturer of Applied Biotechnology, 5-year appointment. African Center for Crop Improvement, School of Biochemistry, Genetics, Microbiology and Plant Pathology. Faculty of Science and Agriculture. Pietermaritzburg Campus, University of Kwazulu-Natal. Ref # SA63/2006
  
  Qualifications: PhD or equivalent degree, in an appropriate field of plant breeding; Experience of supervision of postgraduate students or mentoring of junior staff; Experience in modern molecular techniques. For further information contact the Director, Professor MD Laing, at laing@ukzn.ac.za or visit the website at http://www.acci.org.za
  
  
• Employment opportunities posted on the RiceCAP jobs page.
  
  
• ISMB Calls for SIGs and demonstrations (due 12/15/06) and tutorials (due 5/11/07)
  
  
• Monocots IV. The deadline for symposium proposals is 1st June 2007. The deadline for submission of abstracts for oral contributions and posters will be 31st May 2008.
• Maize Genetics Meeting Call for abstracts and registration coming soon. Abstracts due Feb 2, Registrations due Feb 7.

• MaizeSequence.org is now available!
  
  
• Scientists Unlock Gene in Wheat, Boosting Nutrition Value
  
  
• Worldwide Rice News, from IRRI - definately worth checking out.
  
  
• The Community Sequencing Program : The next deadline for letters of intent for CSP proposals is January 12, 2007. Proposals will be due by March 2, 2007. A letter of intent is required and must be submitted online, beginning December 1, 2006. Submitters whose letters of intent are approved will receive instructions and a proposal template via email.
  
  
• Letter from Dr. Andrew Paterson, 20 Nov 2006
  TO: Anyone interested in the sorghum genome sequence

  As you may know, the US Department of Energy Joint Genome Institute, under its 'Community Sequencing Program' has made rapid progress toward its commitment to provide 8X sequence coverage of the genome of Sorghum bicolor L. genotype, BTx623. These data will be combined with publicly available sequences, assembled into 'contigs' (contiguous sequences without gaps) and 'scaffolds' (reconstructed stretches with any gaps spanned by at least two end-sequenced clones), and integrated with extensive physical and genetic maps to yield genetically-oriented pseudomolecules that are anticipated to substantially cover most sorghum chromosomes.

  Sorghum sequence assemblies will be made available in advance of publication, under the principles of the 'Ft Lauderdale' agreement to protect the interests of scientists who wish to share pre-publication data with the community, i.e. with a request that users defer publication of any whole-genome scale analyses until the sequencing group has published its primary analysis. Leading scientific journals are also being notified. A 4x assembly is now available at https://www.jgi.doe.gov/downloads/Sorghum_bicolor. Use Sorghum_bicolor and ^ico@hgr as login and password, respectively. We anticipate that the genetically- oriented 8x assembly will be available in early 2007, barring unexpected delays.

  A team has been assembled to conduct initial annotation and analysis of the sequence for publication in a leading refereed journal. Although many dimensions of the planned analysis are covered, inquiries about possible participation in this effort should be directed to Dr Paterson (paterson@uga.edu). Team members are responsible for providing their own funding to support their participation.

  Since the primary publication of the sequence will only be able to succinctly describe a few key features, two leading journals have offered to consider companion papers that address specific features in detail, for coordinated publication shortly following the primary sequence, in a 'special section' or perhaps 'special issue'.

  1. Genome Research (www.genome.org/) has agreed to consider large-scale genomic studies that present novel data of biological significance.
  2. The Plant Genome (www.crops.org/genome/) has agreed to consider research that shows clear potential for translating genomic technology into agronomic advancement.

  Both journals will review sorghum genome-related submissions according to their established mechanisms and standards. At an appropriate time, the respective journals will provide further details. We hope that this information is useful in planning for engagement of these new genomic resources for sorghum in your work. We also hope that you share our excitement about these new resources, which promise to add new dimensions to our understanding of botanical and genomic diversity, as well as new opportunities for improvement of leading food, feed, forage & turf, and biofuels crops. We encourage you to consider how the sorghum sequence might fit into your research plans, to submit manuscripts to the coordinated reviews as appropriate, and to contact us with any questions.

  Andrew H. Paterson
  Lead Proposer, CSP Sorghum Sequencing Project
  Chair, Sorghum Genomics Executive Committee
  
  Daniel S. Rokhsar
  Program Head for Computational Genomics
  Joint Genome Institute

  
  
  

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.

• Rice Outlook Report,
• US Wheat Outlook Report and
• Feed Outlook Report (corn, sorghum, barley, oats, hay)
  

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:

• Cold Spring Harbor Laboratory - Meetings and Courses
• GrainGenes Calendar
• IRRI Calendar
• ISCB Worldwide Bioinformatics & Computational Biology Related Events