Previous Hot Topics and Featured Links in GrainGenes





Mapped ESTs from the US NSF wheat EST project
16,000 EST loci mapped in Chinese Spring deletion lines. For additional ways to view and search the map, see our What's New page.


Wheat: The Big Picture
This website describes the life cycle of wheat from germination to harvest. This site has something for everyone and is loaded with beautiful photos of wheat development that users are encouraged to download and use for free. Enjoy!


BarleyBase
A community resource for cereal microarrays
BarleyBase is a USDA-funded public repository for the Affymetrix Barley1 GeneChip expression data. This resource contains information on experiment descriptions, array design, analysis and provides users with the capability to search the contents of the Barley1 GeneChip by sequence and oligo.


Komugi
An Integrated Wheat Science Database.
Komugi has an electronic version of the Wheat Gene Catalogue online, and provides a query interface for gene symbols and markers.


CereGeneDB
A database of coding sequence conservation between rice and nonrice cereals and Arabidopsis.


Western Wheat Quality Laboratory
This site supporting the ARS-USDA Western Wheat Quality Laboratory includes a virtual tour of the laboratory, a description of the Wheat Analysis System (WAS), a Purindoline Genotype Database and much more.


MASwheat Bringing Genomics to the Wheat Field. This site includes protocols for marker assisted selection, papers, collaborators and links.


Gramene: A Comparative Mapping Resource for Grains
Gramene is more than a replacement for RiceGenes. The goal is to benefit all the cereal crops by providing comparative map and sequence data vs. rice. Some data for wheat, barley, oats, maize and sorghum are available already and more to come!

A Tribute to Ernie and Lotti Sears Ernie Sears is regarded by many as the "father of wheat cytogenetics". This tribute was published to accompany the dedication of the Sears Plant Growth Facility at the University of Missouri. Enjoy!


Plant Genomes Central at NCBI
NCBI is making some of the GrainGenes maps of wheat and barley available using their Map Viewer interface, which is especially good for comparing maps side by side and for highlighting markers that have been sequenced.



ITMI Summer Workshop

The International Triticeae Mapping Initiative Summer Workshop was held at Montana State University, Bozeman MT, US, May 29-31, 2005. The new ITMI website includes the slide presentations of the talks.
Wheat physical/genetic integration maps, from Génoplante via Pierre Sourdille.

SSRs and RFLP clones mapped on Chinese Spring deletion lines, and correlated with the Synthetic x Opata, Consensus SSR, and Courtot x CS genetic maps.

GrainGenes 2.0 is here!

If you're reading this and the page is still dingy yellow instead of glistening white, click here for the new GrainGenes website. The old website will continue to be available at http://wheat.pw.usda.gov/ggpages but will no longer be updated. So please switch to the new version, and let us know if you have trouble finding things you're accustomed to finding. GrainGenes 2.0 features the new, relational version of the GrainGenes Database. The old version (now called "GrainGenes Classic") will continue to be available and will continue to be updated daily. A description of the database migration from the ACEDB software to MySQL is here.
Report of the barley CAP planning conference

A conference to plan a Coordinated Agricultural Project proposal on barley translational genomics was held November 13-14, 2004, in Minneapolis MN. The final report from the conference is now available.
Cereal Genomics published

Edited by P K Gupta (CCSU, Meerut, IN) and Rajeev K Varshney (IPK, Gatersleben, DE), this book covers all aspects of structural and functional genomics of cereals. Contents and Contributors.
Comparative Map of Wheat and Rice Genomes

Comparison based on thousands of wheat ESTs mapped in Chinese Spring deletion lines and BLASTed against the rice genome sequence. Supplementary detailed data from Sorrells and La Rota, Genome Research 13:1818-1827 (2003).

www.graingenes.org back online

Nov 27, 2004: The primary server for the "GrainGenes Classic" (AceBrowser) database had a hardware failure on Nov 24 and took some days to repair. It should be fine now; please report any problems.


This is an opportunity to look at the available GrainGenes mirror sites, http://wheat.pw.usda.gov/GG2/pickGG.shtml. The best alternates for GrainGenes Classic are the ones at Saskatoon SK and Albany CA. (But remember that GrainGenes 2.0 is better! And (New) GrainGenes 2.0 has a mirror site too, thanks to our friends at INRA!)
Wheat Genetic Improvement Network, WGIN
Defra, the UK Department for Environment Food and Rural Affairs, is supporting a major public-sector pre-breeding program to deliver genetic material to UK wheat breeders.
Report on IGROW discussions, May 2004
Discussions at the ITMI meeting in Minneapolis.
From Rudi Appels and Bikram Gill.
WMC 1 SSRs

All of the data from the first Wheat Microsatellite Consortium is now online. This includes markers wmc1 through wmc588.

Better Barley Faster: the Role of Marker Assisted Selection
A special issue of the Australian Journal of Agricultural Research, containing results from the Australian National Barley Molecular Marker Program. Abstracts and some articles are available online.

Barley CAP Conference
"Coordinated Agricultural Project Conference on Barley Translational Genomics"
November 13-14, 2004, Minneapolis MN.
The goal of the meeting will be to define research priorities for barley translational genomics and outline a proposal that will be submitted for a barley CAP grant. Everyone who is interested in barley research is invited to attend. Registration is required; however, there is no registration fee. Deadline for registration is October 21.
Announcement and registration form in .doc format
National Research Initiative: Applied Plant Genomics Coordinated Agricultural Project
Fusarium graminareum genome sequenced.
The sequence is available for download and BLAST now. Annotation and analysis later.

Call for Proposals, Competitive Grants Programme for 2005
The GENERATION Challenge Programme: Cultivating Plant Diversity for the Resource-Poor
Deadline for pre-proposals May 15.

NBIC ELECTION UPDATE
Elections for three NBIC regions were held recently. Here are the results.
NORTH CENTRAL REGION: Paul Schwarz, North Dakota State University
NORTHWEST REGION: Pat Hayes, Oregon State University
EAST REGION: Dan Brann, Virginia Tech (retired)

Uniform Regional Scab Nursery 2003 Report is online.
Visit the Germplasm page for this link.

ITMI 2004 Workshop Program and Registration Form   Updated, 12 May
U. Minnesota, Minneapolis, May 22-25, 2004. Click here to download in .doc format. Click here for the first announcement.

Affymetrix Wheat Chip
Individuals who would like specific genes to be represented on the wheat GeneChip can advocate their favorite genes using the Affymetrix request form.

Journal of Agricultural Genomics is back online.
The Journal of Agricultural Genomics (JAG), originally called the Journal of Quantitative Trait Loci, has found a new home. CABI Publishing is now serving the past volumes, with plans to relaunch this journal in 2005.

U.S. Rice Resource Stock Center survey
What are your needs for rice genetic stocks and genomic resources? Please respond to this survey from the US Rice Resources Working Group.

Call for NABGP Pre-proposals
The North American Barley Genome Project (NABGP) is calling for pre-proposals for Fiscal Year 2004. Click here for more information.

Images of Oregon Wolfe Barley Seeds have been added to the OWB Image Gallery
A collection of images from seeds of 94 DH lines and parents were contributed by Nils Stein, Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben.

Summary of Interactive Maps on GrainGenes Now Available
Click Here for a spreadsheet summarizing all 87 maps currently available. Information includes parents, number and type of loci and links to the Map_Data records.

HarvEST:Triticeae version 1.07 released.
The above link will download the HarvEST tool. Visit the HarvEST webpage at http://harvest.ucr.edu for more information. Version 1.07 includes the following features:

 -  ACE alignment viewer - to easily navigate within the CAP3 sequence alignments and find SNP's
-  "Search the Barley Chip" functions and special assemblies related to the barley chip
-  351,656 barley EST and about 1100 other barley sequences
-  Most barley chimeras have been removed from the most current assembly
-  73,689 wheat EST sequences (chimeras are abundant in this assembly)
-  Best BLASTX of GenBank NR and best BLASTX of the translated rice and Arabidopsis genomes, with hyperlinks
-  492 MB download, 640 MB installed
-  Search by expression pattern
-  Extensive "Output Unigene" and other export functions

Phenotypic Associative Microsatellite (SSR) Marker Assisted Selection in barley is now online.
Poster text and tables from Les Wright et al. This is best viewed with Microsoft Explorer.

The 2003 Supplement of the Wheat Gene Catalogue is now online.
Edited by R.A. McIntosh, K.M. Devos, J. Dubcovsky, C.F. Morris and W.J. Rogers.

NSF Wheat EST Genomics Project Resources
Update of the third year for this project to determine the structure and function of the expressed portion of the wheat genomes

Thumbnails of All GrainGenes Images are Now Available
The GrainGenes database and website contains a rich source of images including photos of colleagues, line maps, cytology, pathogens and disease symptoms. Browsing is now easier than ever! Visit the thumbnail directory at http://wheat.pw.usda.gov/ggpages/ggimages.html. Many thanks to Nancy Lui for this effort!

Gramene data on Triticeae
Some Gramene data of particular interest to GrainGenes users:
Comparative genetic maps
Location of Triticeae ESTs on the rice genome sequence

"HarvEST Version 0.82 Just Released"
HarvEST is Windows software to query for ESTs that are differentially expressed among cDNA libraries. The new version contains assemblies with improved separation of paralogs. HarvEST contains data from the U.S. wheat EST project and the U.S. barley EST project.

Triticeae EST-SSR Coordination
A place for communication among those who are mining and using EST-derived microsatellites. Organized by Nils Stein.

More Wheat Genes Galore!
DuPont has released its entire library of 200,000 wheat EST sequences to GenBank. As of November 29, 2002, wheat and barley are the number one and two plant species in the dbEST database, and together they include more ESTs than any other species except human and mouse.

Barley Genetic Stocks database
Gene and allele descriptions from the Barley Genetics Newsletter, compiled in database form by Udda Lundqvist and Morten Hulden. Supported in part by the Nordic Gene Bank.

Cereals Comparative Genomics Initiative program funded by USAID
New! The CCGI now has its own website, www.cerealsgenomics.org.

Genoplante/INRA Wheat SSR Club
Wheat SSR-containing sequences. Sign up to help test and characterize them. Help prevent duplication of effort! Organized by Pierre Sourdille. Updated, 1 February -- More results are available!

2002 Nursery Reports for the Uniform Regional Hard Red Spring Wheat Nursery and The Uniform Regional Scab Nursery are now online.
Visit the "Wheat - Evaluations and phenotyping" sections of the GrainGenes Germplasm page for links to .html and .pdf versions.

Wheat SNP Development
A cooperative project for discovering, testing and characterizing wheat SNPs. Organized by Peter Isaac.
Updated, 12 February -- the third EST assembly, based on 400,000 ESTs, twice as many as previously.

The GrainGenes Mapathon is Underway!
The GrainGenes curator team has organized an all out effort to get the database current with recently published mapping projects. We are happy to announce the addition of the first new maps with dozens more in the "hopper". Click here to see a spreadsheet with an update of all planned interactive GrainGenes maps.

Wheat Genes Galore!
With recent releases of EST data from the International Triticeae EST Consortium (ITEC), the USDA/ARS wheat endosperm sequencing project and the NSF wheat genome project, wheat now ranks 15th among the public entries of EST data according to NCBI with over 46,776 sequences as of November 10, 2000.

Results of ITMI Microarray Questionnaire
From Keith Edwards and Roger Wise.

Arnel R. Hallauer International Symposium on Plant Breeding Just Announced.
17-22 August 2003, Mexico City, Mexico. Click here for the announcement (MS Word format).

Wheat Breeding in the New Century: Applying Molecular Genetic Analyses of Key Quality and Agronomic Traits
A special issue of the Australian Journal of Agricultural Research, containing results from the Australian National Wheat Molecular Marker Program (NWMMP). Abstracts and some articles are available online.

The 2002 Supplement for the Catalogue of Gene Symbols for Wheat is now Online
The 2002 WGC Supplement was organized by R.A. McIntosh, K.M. Devos, J. Dubcovsky and W.J. Rogers. Click here for a link to the update or here for a list of all electronic publications on GrainGenes.

Results of the ITMI Public Workshop, June 2002
A Workshop of the International Triticeae Mapping Initiative was held June 1-4 in Winnipeg, Manitoba. The Proceedings are being assembled here. Please note this link has also been added to the publications page on the GrainGenes website.

Western Wheat Worker Meeting Date Changed
The new meeting dates are June 19th and 20th in Pocatello and Aberdeen. Click here for more information.

Call for papers - 2002 National Wheat Industry Research Forum
The Forum will be held on Jan. 16-17, 2002 and will include both oral and poster presentations. Wheat Industry Conference dates are Jan. 13-18 with general sessions and a trade show Jan. 16th-18th

The 5^th International Triticale Symposium has been announced for June 30 - July 5, 2002.
Click here for Instructions to Authors.

Application of the Molecular Markers in Studies in Plants Workshop
Second Announcement now available. Organised by The Botanical Garden - Centre for Biodiversity Conservation of the Polish Academy of Sciences. The workshop will take place in Warsaw 25-29 Sept., 2002. Original papers will be printed (if accepted by scientific board) in an international journal: CELLULAR & MOLECULAR BIOLOGY LETTERS which is indexed in Chemical Abstracts, AGRO-AGEN, BIOSIS, EMBASE/Excerta Medica and WinSPIRIT.

The Shiri x Galena Barley Mapping Population is now online.
This site provides access to data from this recent study by Marquez-Cedillo and Hayes, and joins other mapping projects with sites on GrainGenes. Click here to access this population or here to see all of the mapping studies on the GrainGenes web site

The International Conference on Bioinformatics (InCoB2002)
has been announced for 6-8 February 2002 in Bangkok, Thailand. Call for papers, sponsors and registration are in progress.
The Barley Harrington x Morex Mapping Population Webpage is now Online
This site provides access to data from this recent study by Marquez-Cedillo and Hayes, and joins other mapping projects with sites on GrainGenes. Click here to access this population or here to see all of the mapping studies on the GrainGenes web site.

The 2001 Wheat Gene Catalogue Supplement is now Online
Click here to load latest supplement by R.A. McIntosh, K.M. Devos, J. Dubcovsky and W.J. Rogers. For all electronic publications available on GrainGenes, select "Publications" from the menu bar above.

Putative/Predicted/Hypothetical Demystified
Ever wonder what the heck was the difference between a putative, predicted and hypothetical gene? According to the Gene List from Cold Springs Harbor, a putative gene has good to exact hits to sequences of known function; a predicted gene is identical to an EST, yet has no ascribed function; a hypothetical gene has no database match. Mystery solved.

Barley mlo Gene Website is Now Online
Erik Schwarzbach has assembled a site about the barley mlo gene for powdery mildew resistance. This includes a list of recent papers on mlo since 1990, a large table with many direct links into GrainGenes for the alleles and genetic stocks involved. Check out the site at http://www.volny.cz/eschwarzbach/

The Wheat Chloroplast Genome Sequenced

The complete sequence of the Chinese Spring wheat (Triticum aestivum L) chloroplast genome is available at the DNA DataBase of Japan. To access the sequence data click here and search for Accession Number AB042240. For more information, or to request a copy of the printed manuscript contact: Dr. K. Tsunewaki or Dr. K. Murai at the Fukui Prefectural University, Fukui, Japan

The Ernie R. and Lotti M. S. Sears Plant Growth Facility naming ceremony
The University of Missouri-Columbia is naming its new state-of-the-art plant growth facility in honor of Ernie and Lotti Sears. The ceremony will be held on May 21, 2001. You're invited!

Marie Curie Training Site in the area of Prevention and Detection of Fusarium Mycotoxins in Cereals selected by the European Commission

The Institute for Agrobiotechnology, IFA-Tulln (Austria) has been selected by the European Commission as a Marie Curie Training Site in the area of Prevention and Detection of Fusarium Mycotoxins in Cereals. Training will be open for PhD students from EU member states as well as all other countries participating in the 5th Framework Programme (mainly states from eastern Europe). Fellowships (Euro 1200 per month) for up to 12 months each are offered by two departments of the IFA-Tulln during a period of four years beginning in October 2000. Information can be obtained at: http://www.ifa-tulln.ac.at/Mycotrain.html

Recent Advances in Wheat Head Scab Research in China
The ARS's National Agricultural Library and the Mycotoxin Research Unit jointly funded this web-based review of recent wheat head scab research in China. The site includes sections on pathogen biology, resistance, disease control and provides several links to other Fusarium projects worldwide.

ITMI to Reorganize
It was decided at the Tenth Public Workshop of the International Triticeae Mapping Initiative (ITMI), held 14-16 June, at the University of Delaware, that a reorganization was in order. Click here for more information


Chromosome aberrations in "Chinese Spring" genetic stocks
Deletions, misidentifications and other things to be aware of when mapping with the classic CS nullisomic-tetrasomic and ditelosomic stocks. From Katrien Devos.

A Table of STS Primers Used for PCR-Mapping of Translocation Breakpoints In Barley is Now Online.
This table, provided by Gottfried Kuenzel, lists the RFLP clone names, STS primer sequences, amplified fragment length, annealing temperature and provides links to the GrainGenes or EMBL records of the clone sequences.

The Standard List for AFLP® Primer Nomenclature is Now Available
This list was generously provided by KeyGene. AFLP® is a registered trademark of Keygene N.V.


Kansas State's Web-based Master in Agribusiness (MAB) program honored as the best new for-credit educational program in the nation by the University Continuing Education Association


The Master in Agribusiness Program (MAB) from Kansas State University, is a distance education program conducted primarily over the internet. Viewing the above link will require Adobe Acrobat (available free at www.adobe.com), or visit the MAB website at www.mab.ksu.edu..

Discussions in Cytogenetics by Charles R. Burnham is now online.

This book provides detailed discussions on topics including changes in chromosome structure (inversions, duplications, etc.), number (aneuploidy, polyploidy, etc) as well as special sections on sex-determination and apomixis. Originally copyrighted in 1962, this online version was reproduced from the hand-annotated sixth printing in 1980. Click here for more information, or go directly to the table of contents

ITEC: International Triticeae EST Cooperative

A project to develop a pool of 40,000 Expressed Sequence Tags (ESTs) from the Triticeae and to make them publicly available by 1 July 2000..

GrainTax: Triticeae taxonomy

The Wheat Synonymy Tables Project

Publications

Grains-related Newsletters, Journals, Bulletins, articles, monographs, nomenclature recommendations

KOMUGI

U.S. Mirror of the KOMUGI database of genetic stocks for Triticum, Aegilops and Avena. Courtesy of the Wheat Network of Japan.

Wheat and Barley Improvement for the Next Century

Priority Needs for Biotechnological Approaches to Wheat and Barley Improvement

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