Current NewsGramene News ArchivePast and Upcoming Outreach

April 2002 - May 2006 News

News Update 5/06



New Publications!

Gramene Release #21 - May 2006

Gramene workshop at RiceCAP

News Update (3/02/06)

Release #20 of Gramene in March 2006

RTWG workshop materials are available from the Gramene Outreach Page. Materials include the workshop presentation and exercises, as well as the Gramene poster.

Some new publications from the literature database that you may wish to check out:
News Update (1/04/06)

The GSOR is a distribution site for Nipponbare. Nipponbare seed is available for molecular studies. This material, grown in Stuttgart, is descended, via Cornell, from the single plant selection identified by Dr. T. Sasaki of Japan, for the International Rice Gene Sequencing Project. For molecular studies, it is deemed critical that Nipponbare seed must be descended from the Sasaki selection. Researchers may request samples of the Nipponbare through the GSOR: gsor@ars-grin.gov.


Gramene announces release of new website layout.
Based upon the needs of and feedback from Gramene users, we would like to announce the release of a new look to the Gramene home page and navigation.

Gramene’s new navigation bar now uses drop-down menus and the following navigation:

Other Home Page features include:

To learn more about Gramene Navigation, review the navigation tutorial.

Attend a Gramene workshop!:
Gramene workshop at the Plant and Animal Genome XIV Conference on Jan 17, 2006.
Gramene workshop at the 31st annual Rice Technical Working Group meeting on Feb 25, 2006

To read Gramene's most recent publication see
(Gramene Reference ID 11021) P. Jaiswal, J. Ni, I. Yap, D. Ware, W. Spooner, K. Youens-Clark, L. Ren, C. Liang, W. Zhao, K. Ratnapu, B. Faga, P. Canaran, M. Fogleman, C. Hebbard, S. Avraham, S. Schmidt, T. M. Casstevens, E. S. Buckler, L. Stein, and S. McCouch (2006), Gramene: a bird's eye view of cereal genomes, Nucleic Acids Research, 2006 Jan 1;34(Database issue):D717-23.

News Update (12/8/05)
Recent literature additions include: Stay current with literature in the Literature Database.

Rice News Worldwide from IRRI

Biofortified, iron-rich rice improves nutrition in women and Fortified Rice Helps Combat Malnutrition

Open Source Agriculture -(article on Patents and Biotech)
Gramene Release 19.0. October 31, 2005 (More info)
This release includes new or updated data and software from Gramene.

Gramene Database:

Database statistics can be accessed here.

Genomes: This build brings many updated and new mappings to the database. Also notable are changes in the ContigView, changes to make track names more intuitive and consistent, and a new Oryza Sativa TE (transponsable element) track added at the bottom of the detail view.

Maps: In this build, we present our initial release of the IRGSP build 4.0 rice genome assembly, have added RFLP markers from rice, added three maps of the recently-released set of Class I SSRs, updated the TIGR rice assembly; updated 9 rice maps with genes and QTL, and added a QTL map for maize.

Markers: The database has been updated with an additional 13,519 Class I SSRs from rice; 2,530,661 Genbank dbEST sequences from fifty species of Poaceae as marker type "EST"; 129,527 NCBI Unigene entries from six Poaceae species; 472,408 TIGR Gene Indexes from eight Poaceae species as marker type "EST Cluster"; and 91,074 GenBank DNA sequences from Poaceae flagged as mRNA (excluding dbEST) entries from 162 species as marker type "mRNA".

Proteins: The protein database includes new and updated information on 68,123 gene products drawn from SwissProt (2,074) and SP-TREMBL (66,049). These proteins are annotated using Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro categories. A total of 49,565 gene products are associated with 1,479 Gene Ontology terms.

Ontologies: The Gene (GO), Plant (PO and GRO), Trait (TO), Environment (EO) and taxonomy (GR_tax) ontologies were updated with their most recent version, including the addition of new terms and annotations. The ontology detail page displays were updated to show external references and comments associated with a given ontology term. e.g. NADP-malic enzyme C4 photosynthesis (GO:0009762) has references linking to PubMed (PMID:11788762) and Pathway (MetaCyc:PWY-241).

Genes: This release presents a reorganized gene detail display page, and additional curated and mapped genes.

QTL: For release 19, there are newly curated rice QTLs from recent publications and newly imported maize QTLs from MaizeGDB; Trait Ontology (TO) terms have also been integrated

    Gramene Release 19.0 expected late October. (10/11/05)

To bring more data into Gramene for the upcoming PAG meeting, we are going to postpone our planned release 19.0 for 1-2 weeks. We know that the upcoming additions and updates are eagerly anticipated. We are sorry for the extended waiting this will bring to you, and thank you for your support. Subscribe to Gramene-Announce to be kept up-to-date on Gramene News!

    Upcoming Events: (10/11/05)

Plant and Animal Genome XIV Conference, January 14-18, 2006, San Diego, CA, USA
  • 1/17/06 Workshop: Using Gramene (More Info), and several posters

    • Rice Technical Working Group Meeting, Feb. 26-Mar. 1, 2006, The Woodlands, Texas, USA

         Recent additions to the Gramene Literature Database. (10/11/05)

    Architecture of floral branch systems in maize and related grasses. Vollbrecht E, Springer PS, Goh L, Buckler ES 4th, Martienssen R. Nature, 2005, 436, pp.1119-1126.

    Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Bowers-J-E, et al. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102, pp.13206-13211.

        Coming Soon! Gramene Release 19 is expected in October 2005! (9/23/05)

         The September RiceCAP Newsletter is available online. (9/23/05)

         Nepal farmers reap bumper harvest.
    Farmers in Nepal are the latest to reap huge benefits from an ingenious method of rice cultivation. Article on "System of Rice Intensification" or SRI. From BBC News 9/2/05(9/23/05)

         New in the Literature Database (8/23/05):

        Gramene Release 18.0. July, 2005 (More info)
    This release includes information on new or updated data and software from Gramene.

    Gramene website features:
    "Mutant" link on the navigation bar replaced with "Gene".

    Gramene Database:

        Look for Gramene at Plant Biology 2005 meeting (July 16-20, 2005), Seattle, Washington, USA. July, 2005

        1st International Biocurator Meeting. Pacific Grove, CA. December 8-11, 2005.June, 2005
    This meeting will provide a forum for curators and developers of biological databases to discuss their work, promote collaboration, and foster a sense of community in this very active and growing area of research.

        Gramene Release 17.a. May, 2005
    This is an interim release with addition of Ensembl Browser for maize and Arabidopsis (and Ensembl Compara data between rice and these two species) (details)

        New Gramene Website Features, April, 2005

        Gramene Release 17.0. March, 2005
    This release includes information on new or updated data and software from Gramene.
    Gramene website features:

    Gramene Database:

        WORKSHOP ON CEREAL GENOMICS March, 2005
    This one-week workshop on Cereal Genomics will enable participants to take advantage of emerging genetic tools and genomics data in the cereals, including the complete genome sequence of rice and extensive EST and genome survey sequence from maize, wheat and other grasses. September 13 - 19, 2005
    Application Deadline: May 15, 2005.

        Oryza News March, 2005
    Robert Zeigler has been named as the next Director General of IRRI.

        Interesting Oryza Publication, February, 2005
    The Genomes of Oryza sativa: A History of Duplications

        Interesting Oryza Publications, February, 2005

        Gramene presentations at the Plant and Animal Genome XIII Conference, January 15 - 19, 2005  

        5th International Rice Genetics Symposium. December 2004
    This symposium, held every five years, will also include the Third International Symposium on Rice Functional Genomics. November 19-23, 2005, Manila, Philippines.

        Gramene Release 16.0. December 2004 (More info)
    This release includes information on new or updated data and software from Gramene.

    Gramene website features:
    Gramene Tips - Helpful tips on using the Gramene Database are now located on the home page.

    Gramene Database:

        Maize Transformation Workshop. March 7-10, 2005. Madison, Wisconsin, USA

        Rice in the News    October 2004

        Gramene Release 15.0    October 2004
    This release includes information on new or updated data and software from Gramene. (More info)

    Gramene website features:

    These pages can be accessed from How to Use Gramene and the Site Map.

    Gramene Database:

        Plant Genomes: From Sequence to Phenome    September 2004 Conference to take place at Cold Spring Harbor Laboratories December 9-12, 2004. Abstracts due October 8, 2004.

        NSF Plant Genome Research Program    September 2004 The FY2004 awards have been made and can be viewed here. The Program Solicitation for FY2005 is available here.

         September is National Rice Month   Learn more here.

         Gramene Release 14.0   August 2004
    This release includes information on new or updated data and software from Gramene.

    Gramene website features:

    Gramene Database:

        Gramene workshop at Plant Biology 2004, July 25th   

        Meeting Announcement  June 14, 2004
        2nd International Symposium on Rice Functional Genomics, Tucson, AZ, November 15-17th, 2004 (More info)

         Gramene Workshop Tutorials.  March 04, 2004
    Click here for details.

        Gramene will be presenting hands-on computer sessions involving bioinformatic exercises at Maize Genetics, Genomics and Bioinformatics Workshop at the CIMMYT International Research Center in Mexico from March 7-11, 2004.  March 04, 2004
    For more information contact Gramene representatives Dr. Doreen Ware or Dr. Susan McCouch.

        46th Maize Genetics Conference, Mexico City, Mexico, March 11-14, 2004  March 04, 2004

        Gramene participated in a demonstration workshop at the Pan-American Studies Institute for Bioinformatics on February 9-20, 2004 in Montevideo, Uruguay.  March 04, 2004

        Genetic Stocks - Oryza (GSOR) Collection.   
    The GSOR was established in August 2003 to collect, preserve, and distribute, on request genetic materials that might otherwise be lost as researchers retire and/or grants terminate.

        United Nation's Food and Agriculture Organisation (FAO) celebrates the year 2004 as its INTERNATIONAL YEAR OF RICE.   

        Rice research enters the space age.  

        Gramene Release 13.0    January, 2004.
    The new release includes information on new or updated data and software from Gramene.

    Gramene website features:  

    Gramene Database:

        Gramene presentations at the Plant and Animal Genome XII Conference, January 10 - 14, 2004  

        World's 'oldest' rice found, a BBC report  
    Scientists have found the oldest known domesticated rice. The handful of 15,000-year-old burnt grains was discovered by archaeologists in Korea. More info

        Job Posting:   
    Plant Biology Curator with Gramene database at Cornell University   more info

        U.S. Rice Resource Stock Center  
    Are you interested in rice genetic stocks and genomic resources? If so please click here for more detail.

        Gramene Release 12.0   September, 2003.
    The new release includes information on new or updated data and software from Gramene.

    Gramene website features:  

    Gramene Database:

        Interesting publications    July 30, 2003
    Mitochondrial complex I from Arabidopsis and rice: orthologs of mammalian and fungal components coupled with plant-specific subunits
    Biochimica et biophysica acta , 2003, 1604, pp.159-169

    A pentatricopeptide repeat-containing gene that promotes the processing of aberrant atp6 RNA of cytoplasmic male-sterile rice
    FEBS letters , 2003, 544, pp.99-102

         Interesting publications    July 18, 2003
    Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice
    Science, 2003 July 18; 301: 376-379.

    In-Depth View of Structure, Activity, and Evolution of Rice Chromosome 10
    Science, 2003 June 6; 300: 1566-1569.

        Interesting publications    May 15, 2003
    Towards an analysis of the rice mitochondrial proteome
    Plant Physiol, 2003, 132, 230-242

    Expression of novel rice gibberellin 2-oxidase gene is under homeostatic regulation by biologically active gibberellins
    J Plant Res, 2003, 116, 161-164


    The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa
    Nucleic Acids Res, 2003, 31, 2601-2613

    Control of tillering in rice
    Nature, 2003, 422, pp.618-621

    The OsTB1 gene negatively regulates lateral branching in rice
    The Plant journal, 2003, 33, pp.513-520

    Salinity tolerance of japonica and indica rice ( Oryza sativa L.) at the seedling stage
    Planta, 2003, 216, pp.1043-1046

        The CMap comparative map viewer has been updated, March 12, 2003
    Feb. 28, 2003

        Interesting publications

        Development of plans for a Rice Resource Center in USA: A report  
    Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.)
    DNA RESEARCH 9, 6, pp. 199 - 207 (2002)
    Design and application of microsatellite marker panels for semiautomated genotyping of rice (Oryza sativa L.)
    Crop Sci 42:2092-2099

        Release 11.0 of Gramene, January 29, 2003, with updates of the Sequence and Protein databases
    For database statistics see here

        Gramene presentations at the Plant and Animal Genome XI Conference, January 11 - 15, 2003

        Gramene publication, Dec. 12, 2002
    Gramene, a Tool for Grass Genomics
    Plant Physiol, December 2002, Vol. 130, pp. 1606-1613

        The sequencing of rice chromosomes 1 and 4 have been completed, Nov. 21, 2002
    Sasaki et al. 2002
    The genome sequence and structure of rice chromosome 1
    Nature 420: 312 - 316
    Feng et al. 2002
    Sequence and analysis of rice chromosome 4
    Nature 420: 316 - 320

        Interesting publications, Nov. 13, 2002
    Expression of alpha-Expansin and Expansin-Like Genes in Deepwater Rice
    Plant Physiol. 2002 Nov;130(3):1396-1405
    The Procambium Specification Gene Oshox1 Promotes Polar Auxin Transport Capacity and Reduces Its Sensitivity toward Inhibition
    Plant Physiol. 2002 Nov;130(3):1349-1360
    Isolation and characterization of a rice dwarf mutant with a defect in brassinosteroid biosynthesis
    Plant Physiol. 2002 Nov;130(3):1152-1161
    Inventory and Functional Characterization of the HAK Potassium Transporters of Rice
    Plant Physiol. 2002 Oct;130(2):784-795
    Long terminal repeat retrotransposons of Oryza sativa
    Genome Biol , 2002, 3, pp.RESEARCH0053-RESEARCH0053
    Mosaic organization of orthologous sequences in grass genomes
    Genome Res. 2002 Oct;12(10):1549-1555

        Release 9.0 of Gramene, September 30, 2002, with updates of the Sequence and Protein databases
    The Rice Sequence database now contains 2,680 Phase 2 or 3 Clones from Genbank, with 14,712 annotated Genes (12,939 of these have a corresponding protein in the protein database) and 59,853 FgenesH predictions (4,837 of these have a corresponding protein in the protein database)
    The Rice Protein database now contains 12310 Proteins (10523 of these have at least one corresponding Gene in the sequence database)
    Updated Code for the Gramene website is available HERE
    Updated Data Export is available HERE

        Comparative Map Viewer, September 16, 2002
    The new release of our Map Search database currently holds ten genetic maps of rice, four genetic maps of maize, one map each of barley, oat, wheat and sorghum and two physical maps of rice, including the integrated FPC map (I-Map), and the CUGI maize FPC map. The new release of the Comparative map viewer contains three new features of interest:

        Rice Genes and Alleles Database, September 13, 2002
    We are pleased to announce the first release of the Rice Genes and Alleles Database including entries on 424 genes characterized by phenotypes. The descriptions include information from published reports on their alleles, associations to trait, plant and gene ontologies, map positions, linked markers, images and sequences. User can search for the gene symbol or gene name by using Gramene phenotype Search.

        Ontology Database, September 13, 2002
    Plant OntologyTM for Rice Version 1.0. The first version of Gramene plant anatomy and rice growth stage ontology is available. The ontology terms have associations to rice phenotypes describing:
    Trait OntologyTM for Rice version 2.0 ( BROWSE )
    Gene OntologyTM August release ( BROWSE )

        Interesting publications, September 11, 2002
    Efficient gene targeting by homologous recombination in rice
    Nature biotechnology, 2002
    Biolistic mediated site-specific integration in rice
    Molecular Breeding, 2002, 8(4), pp.345-349
    A new approach for the identification and cloning of genes: the pBACwich system using Cre/lox site-specific recombination
    Nucleic acids research, 2000, 28, pp.19-19

        Interesting publications, August 25, 2002
    Proteomic survey of metabolic pathways in rice
    PNAS, 2002
    Molecular mapping and genetic analysis of a rice brown planthopper (Nilaparvata lugens Stal) resistance gene
    Hereditas, 2002, 136, pp.39-43
    Characterization of a HKT-type transporter in rice as a general alkali cation transporter
    The Plant journal : for cell and molecular biology, 2002, 31, pp.529-542

        Updated wheat EST alignments, June 21, 2002
    A total of 166,513 wheat ESTs from dbEST where compared to 1,861 sequenced rice BAC/PAC clones. The resulting alignments represent 49,146 triticum aestivum EST sequences.

        Interesting publication, June 20, 2002
    Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project
    Nucleic Acids Research, 2002, 30, pp.2316-2328

        Interesting new reports on rice, June 7, 2002
    A fine physical map of the rice chromosome 4
    Genome research, 2002, 12, pp.817-823
    Transgenic rice is a source of iron for iron-depleted rats
    The Journal of nutrition , 2002, 132, pp.957-960
    Africa looks to new breed of rice to combat food shortages
    Lancet , 2002, 359, pp.1320-1320

        Trait OntologyTM for Rice Version 1.7
    Available on Ontology Browser, May 28, 2002.

        Release 5.0 of Gramene, April 29, 2002, with updates of the Sequence and Protein databases
    The Rice Sequence database now contains 1780 Phase 2 or 3 Clones from Genbank, with 8160 annotated Genes (7957 of these have a corresponding protein in the protein database)

    The Rice Protein database now contains 8985 Proteins (6912 of these have at least one corresponding Gene in the sequence database)

    Code for the Gramene website is available HERE

        The "Gramene-announce" mailing list April 22, 2002.
    Subscribe to the Gramene-announce list to receive announcements of updates to the Gramene site.

        Rice "Green Revolution Gene" Identified April 18, 2002.
    Nature 2002 April 18; 416 :701-702 (more info)
    DNA Research 2002 Feb 28;9(1):11-7 (more info)

        Indica Sequence Available for Blast Search
    <\a>
    April 11, 2002

        Syngenta and Beijing group publish draft sequences of the rice genome
    A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica), Science, Vol 296, 2002
    A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica), Science, Vol 296, 2002

        Improved Gene Ontology Browser
    Association "Display" and "Download" features have been added to the Ontology browser, March 22.

        New Publication
    Gramene: development and integration of trait and gene ontologies for rice, March 16.

        First Release of Rice to Gene Ontology Associations
    >Associations,  On GO Consortium, March 7.

        New Release of Rice Protein Database
    Release 4.1.0, Feb. 25.

        New Publication
    Gramene: a resource for comparative grass genomics, 2002