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September 2006 Newsletter

September is National Rice Month in the USA.

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:

Gramene's Diversity Module
Postdoctoral Associate - Job opportunity
Recommended Reading from the Gramene Literature Database
Gramene FAQ

Community News:

Calls for Papers
Check out the latest...
Rice Outlook
Community Calendar

Gramene News

Gramene's Diversity Module: Key Information for Breeders Working Toward Crop Improvement.
Written by: Isaak Tecle, Gramene Curator
Genetic diversity is essential for the continued genetic improvement of plants. Genetically variable germplasms serve as a source of rare or unique alleles that can be introgressed into elite cultivars in order to introduce new traits or to enhance innate traits. Therefore, conservation and utilization of the genetic diversity of a species is necessary to ensure the increase in crop production required to meet growing global need for food.
Identifying germplasms with alleles variant in a locus underlying phenotypic variation for a trait of interest is a challenge to a plant breeder's effort to achieve genetic improvement. To this end, DNA-based marker analysis is employed to help unravel the genetic variation in germplasms. Simple sequence repeat (SSRs) variations, single nucleotide polymorphisms (SNPs), and restriction fragment length polymorphism (RFLPs) are among the DNA-based genotyping approaches used to evaluate genetic variation in crops.
Progess is being made! There is an increasing amount of genetic diversity data being generated and published in today's scientific literature. At the Gramene database, the genetic diversity module ( has been created to collect, organize, store and make publicly accessible this genomic diversity data of cereal crops.
Currently, the database contains SSR and SNP allelic data and passport descriptions for rice, maize and wheat germplasms. It also holds phenotypic data for maize. In the future, phenotype data for rice will also be curated. Simple sequence repeat or single nucleotide allelic variation across loci of a germplasm or in a locus across multiple germplasms can be found by searching for germplasm accession number, accession name or marker/locus name.
The database is updated approximately 4 times a year.
Job Opportunity - Postdoctoral Associate - 05677
Job Description

Gramene database (, is seeking applicants for a full time position for a plant biology curator who will participate in the development and maintenance of structured vocabularies for describing plant morphology, anatomy, growth and development stages for its Plant Ontology Consortium (POC) project ( These vocabularies (ontologies) are necessary to provide the backbone for describing phenotypes and gene expression patterns, and allow database users to perform a set of common queries or searches across different plant databases. The Plant Ontology Consortium is a collaboration among plant genome databases related to rice, Arabidopsis, maize, legumes, Solanaceae, etc.

The successful candidate will work with a team of curators, software engineers, and database developers at Gramene and collaborating database projects, such as TAIR ( and MaizeGDB (; contribute to annotation of phenotypes, germplasm and gene products by using the vocabularies developed in the project; participate in development and application of methods to improve consistency and to enhance the quality of annotations; promote the use of ontologies in comparative genomics and biology through active participation in workshops, seminars and scientific meetings.


Successful candidate will have a Ph.D. degree and training in Plant Biology and related fields (e.g. Systematics, Development, Physiology), a demonstrated ability for independent, critical thinking and excellent communication and teamwork skills. The curator must be able to travel to and attend 2-3 national and international meetings per year. Familiarity with biological data mining, basic UNIX/Linux commands, spreadsheets, and commonly used biological research tools is desired. A working knowledge of SQL would be an asset but not required. Qualified candidates should e-mail a cover letter and resume to Pankaj Jaiswal (

Recommended Reading
  • Genomic and Genetic Characterization of Rice Cen3 Reveals Extensive Transcription and Evolutionary Implications of a Complex Centromere. Yan et. al. The Plant Cell, 2006. More Info)
  • n RNA-dependent RNA polymerase is required for paramutation in maize. Alleman, M. et. al. Nature, 2006, 442, pp.295-298. ( More Info)
  • Mapped Ds/T-DNA launch pads for functional genomics in barley Zhao, T. et al. The Plant Journal, 2006. ( More Info)
  • Conserved requirement for a plant host cell protein in powdery mildew pathogenesis. Consonni, C. et al. Nature genetics. ( More Info)
  • Rice NTRC Is a High-Efficiency Redox System for Chloroplast Protection against Oxidative Damage. Perez-Ruiz, J. M. et al. The Plant cell, 2006. ( More Info)
  • The genetic basis for differences in leaf form between Arabidopsis thaliana and its wild relative Cardamine hirsuta. Angela Hay & Miltos Tsiantis. Nature Genetics 38, 942 - 947 (2006)

    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. Here are some recent questions that have been answered.
    Q -Where can I find information about the history of a germplasm accession "RA####"?

    A - Please refer to the Gramene Diversity database to find the germplasm information (country of origin, collection date etc...) Gramene has for the accessions. The RA- numbers are stock numbers assigned to the accessions in Dr. Susan McCouch's lab; you will find more identification including their common names, accession numbers assigned to them at IRRI/IRIS and NSGC/GRIN. For additional information the IRIS and GRIN databases may have about the germplasms, click the "search at IRRI" or "search at GRIN" links.

    Community News

    Calls for Papers

  • The January 2007 issue on "Genomics: moving towards gene revolution in rice" for "Physiology and Molecular Biology of Plants", an Indian journal is under review. I (Rajinder Kumar Jain) take this opportunity to call for the short review articles, research papers, notes, etc. for this special issue. For details you may visit The last date of submitting the articles is August 31, 2006.

  • PAG Abstracts and Posters: All accepted abstracts are limited to 250 words and will be included in the final printed program. The abstract submission deadline for PAG-XV Posters is Monday, 2 October, 2006, please submit your abstract now while space is still available (Over 1000 Abstracts are expected). Due the large number of abstracts, space availability may depend on the date of the abstract submission. Electronic web submission is preferred.

    Check out the latest news:
    • Plant Biology Databases: A Needs Assessment - White Paper This is a summary of a collaborative review the anticipated needs of the plant genome research community for long-lived data collections. The authors offer guidelines for balancing the funding of data production projects with those aimed to manage and integrate the data. In particular, there is a pressing need to develop a trained cadre of skilled knowledge workers who are able to curate complex biological data, and to provide this cadre with a system of stable funding that enables data repositories to be established and maintained over extended periods of time. There is a positive current trend of species-specific databases to expand into comparative genomics-minded clade-oriented databases, but the authors caution that new technologies are needed to facilitate the transparent integration of data among these databases.

    US Rice Outlook (From 8/11/06

    USDA's first survey-based forecast of the 2006/07 U.S. rice crop is 197.2 million cwt, down almost 3 million cwt from last month's projection, and down 26 million cwt from 2005/06. Average yield is forecast at 6,813 pounds per acre, down 95 pounds per acre from last month. Long- grain production is forecast at 147.9 million cwt, down 6.1 million cwt from last month, while combined medium- and short-grain production is forecast at 49.3 million cwt, 3.3 million cwt above last month. U.S. 2006/07 exports are projected at 97 million cwt, down 3 million cwt from last month. Domestic and residual use is nearly unchanged from a month ago. Ending stocks are projected at 22.7 million cwt, down slightly from last month. The season- average farm price is projected at $9.25 to $9.75, up 10 cents per cwt on each end from last month.

    Projected global 2006/07 production is lowered, consumption is raised, and trade and ending stocks are nearly unchanged from a month ago. World 2006/07 rice production is projected at a record 417.8 million tons, 0.5 million tons below last month. The decline in the world rice crop is due primarily to reduced production in Vietnam, North Korea, and the United States, which is partially offset by an increase for Thailand. World 2006/07 ending stocks are projected at 79 million tons, nearly the same as last month.
    For more indepth information, see:

    Upcoming Meetings
    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 ( 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 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