October 2006 Newsletter

• Gramene demo/workshop
• Posters on Gramene Updates, Biochemical Pathways, Genetic Diversity, Ontologies, and the Species pages.

• Gramene: A Genomics and Genetics Resources for Maize.
  Jaiswal et. al. Maize Genetics Cooperation Newsletter, Volume 80, 2006.
  [Full article] or [PDF Newsletter, pp 99-107]
  
  
• Mutations in the eIF(iso)4G translation initiation factor confer high resistance of rice to Rice yellow mottle virus.
  Albar et al. Plant J. 2006 Aug;47(3):417-26. Epub 2006 Jun 15.
  [PubMed]
  
  
• Genetically modified crops. Tracing the transatlantic spread of GM rice.
  Vogel. Science, 2006, 313, pp.1714-1714. [More Info]
  
  
• Crystal structure and activities of EXPB1 (Zea m 1), a {beta}-expansin and group-1 pollen allergen from maize.
  Yennawar et al. Proceedings of the National Academy of Sciences of the United States of America, 2006. [More Info]
  
  
• Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B.
  Paux et al. The Plant journal: for cell and molecular biology, 2006. [More Info]
  
  
• Distinct patterns of control and expression amongst members of the PEP carboxylase kinase gene family in C plants.
  Shenton et al. The Plant journal : for cell and molecular biology, 2006, 48, pp.45-53. [More Info]
  
  
• In plants, highly expressed genes are the least compact.
  Ren et al. Trends in Genetics, 2006, 22, pp.528-532. [More Info]

Q I am very impressed with the genomes update to TAIR6 and TIGR4. I am particularly interested in the orthologs. Could you please explain the one2many. Does it mean many in rice or arabidopsis? The peptide length for the arabidopsis genes is one more than the peptide length reported in TAIR. Why?
A The best documentation for the method used to compute orthologs is found here; http://www.ensembl.org/info/data/compara/homology_method.html The 'one2many' relationship, however, is not directional. I.e. it could be that one arabidopsis gene has many rice orthologs, or vice-versa. This is a known limitation of the data model, and may be addressed later on. For the peptide length, Ensembl counts the final stop codon, whereas I suspect that TAIR does not.

Q I can see in the rice / maize genomic viewer that QTLs are mapped to a specific sequence location. can this mapping be downloaded ? if yes, where from ?
A ftp://ftp.gramene.org/pub/gramene/release22/data/qtl/Rice_QTL.dat

Q I implemented the Omics viewer as directed by the procedure in your tutorial. However, I get the error message which is " " is not a valid integer. What does this message mean?
A I have a feeling that this error is due to you not entering a number in the " ata column (numerator in ratios):" (see slide 29 of the tutorial). Generally the first column (that contains the LOC identifier) is known as column 0, and the first data column will be 1, the second column 2, etc. Hopefully be entering the number(s) of the column that you wish to view in the data column, you will overcome this problem.

University of Florida's Gulf Coast Research and Education Center is seeking a postdoctoral research associate to conduct disease resistance evaluation and inheritance studies in conjunction with plant breeders and pathologists. The project aims at inheritance study of host plant resistance to fungal diseases in caladium and gerbera and selection of new disease-resistant breeding lines. Research activities include protocol development for evaluation of resistance to fusarium tuber rot and pythium root rot, assessment of resistance in commercial cultivars, breeding lines, and segregating populations, and determination of the mode of inheritance and heritability parameters. Molecular marker and QTL analysis may be involved in the research. Ph.D. in plant genetics and breeding, horticulture, or plant pathology is required. Experience with fungal culture, fungal disease resistance evaluation, quantitative genetic analysis, and molecular marker analysis is desirable.

To apply, send CV, cover letter and names and addresses of three references to Zhanao Deng at zdeng@ufl.edu, or University of Florida, Gulf Coast Research and Education Center, 14625 C.R. 672, Wimauma, FL 3 33598. http://gcrec.ifas.ufl.edu/.

• Test your Agricultural Research Knowledge
  
  
• RiceCAP newsletter [pdf]
  
  
• IRRI Press release: Typhoon Blasts Rice Research Institute
  
  
• Rice Today, IRRI's international magazine dedicated to rice-related research for development. Oct-Dec 2006 is now available online.
  
  

RICE: Note: The market impact of genetically engineered rice found in U.S. long-grain supplies is considered in this report.

U.S. rice production in 2006/07 is forecast at 193.3 million cwt, 4 million cwt below last month due entirely to a reduction in area. Harvested area is estimated at 2.8 million acres, 72,000 acres below last month. The average yield is estimated at 6,846 pounds per acre, up 33 pounds per acre from last month. Long-grain production is estimated at 143.6 million cwt, down 4.3 million from last month. Combined medium- and short-grain production is estimated at 49.6 million cwt, up 0.3 million cwt from a month ago. All- rice beginning stocks are raised 8.6 million cwt from last month. Domestic and residual use is lowered 4.5 million cwt from a month ago based in part on the decline in 2005/06. Rice exports for 2006/07 are projected at 97 million cwt, unchanged from a month earlier. Compared with last month, forecast exports to some markets are reduced while exports to others are increased. The ending stocks are projected at 31.9 million cwt, 9.2 million cwt above last month. The season-average farm price is lowered $0.50 per cwt on each end to $8.75 to $9.25 per cwt compared to $7.62 per cwt in 2005/06.

On August 30 the National Agricultural Statistics Service (NASS) estimated August 1 U.S. rice stocks at 43 million cwt (rough-equivalent basis), 8.6 million cwt above last month's projection, and 5.30 million cwt above a year earlier. NASS estimated rough rice stocks at 37.4 million cwt and milled rice stocks at 3.9 million cwt.

Global 2006/07 rice supply and use are little changed from a month ago. Ending stocks are projected at 79.4 million tons, 0.4 million above last month, but down 1 million tons from 2005/06. The increase in ending stocks from a month ago is due mainly to larger U.S. stocks.

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

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.

October 9-13, 2006, 2nd International Rice Congress, New Delhi, India Includes The 25th International Rice Research Conference, The World Rice Commerce Conference, and The 2nd International Rice Technology and Cultural Exhibition

October 11-14, 2006. PlantGEMs Congress will be held in Venice. The Plant Genomics European Meetings (Plant GEMs) is a forum and communication platform for European plant genome researchers. It is open to interested scientists from all over the world. Since the creation of the ERA-PG (European Research Area in Plant Genomics) network in 2004, Plant GEMs has played a major role in fostering new collaborations and in stimulating networking among national genomic programs.

January 13-17, 2007. Plant and Animal Genome XV Conference

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.

February 1-2, 2007. Beneath the Hull: Exploiting the Health-Beneficial properties of the Rice Grain. New Orleans. A rice utilization workshop.

January 12-16, 2008. PAG-XVI

See also:

• Cold Spring Harbor Laboratory - Meetings and Courses
• GrainGenes Calendar
• IRRI Calendar