What's new in GrainGenes? -- 1997

09 December 1997

Hahna Kang has joined the GrainGenes crew in Albany, CA, filling the position previously held by Jon Wong. She has started by converting volumes of the Annual Wheat Newsletter to HTML format, see below.

GrainGenes Database

- 45 wheat microsatellites, from Victor Korzun Now have a total of 56 WMS primers. "find probe wms*"

- 60 PSR probes, including their Polymorphisms, Mapped_bands and Synonyms from Mike Gale and Katrien Devos

- Rye map, from Victor Korzun Map_Data "Rye, P87 x P105"

- Rye map, from Senft and Wricke,Plant Breeding 115:508, 1996 Map_Data "Rye, Hannover"

- Chromosome 2H translocation breakpoints, from Gottfried Kuenzel Query 'find image "2h translocation breakpoints"'.

- High-resolution map of the Pc71 region of oat, from Arla Bush 'find linkage_data "Oat, D526 x Lang"'

- Corrections and updates submitted via the online "Submit comment" form, from Udda Lundqvist, Konny Richter, Tim Close, David Marshall and others. Many thanks!

- Windows95/NT version of GrainGenes available for downloading from the Korea Rice Genome Database Network, ftp://bioftp.myongji.ac.kr/pub/graingenes/WinGrainGenes/GrainGenes.zip Also available on CD: send requests to Dr. Biek Hie Nahm, Myongji University, Yongin, Korea, bhnahm@bioserver.myongji.ac.kr.

Gopher

- Wheat performance evaluations

- Western Regional Performance Nursery Program - 1998 Entry Lists, from Jim Anderson

- State Performance Tests - New York, 1997

- Wheat quality evaluations

- Molecular and genetic data - Compendium of wheat lines carrying rye chromosome arm 1RS Updated with 170 new lines from the 1997 nurseries, from Bob Graybosch

- Maps and mapping data - Hordeum - Barley gene map, 7-chromosome Updated according to BGN 26. Thanks to Udda Lundqvist.

GrainGenes Webserver

- HTML version of Annual Wheat Newsletter volumes 41 and 43. (The searchable and word-processor versions will still be maintained on the Gopher server.)

Other sources of interesting information

- The new release of RiceGenes contains comparative maps vs. the Triticeae "find map_data triticeae-consensus"

- Triticale information, from Kath Cooper http://www.waite.adelaide.edu.au/Plant_Science/labs/kcooper/kcooper.htm

- Cooperative Research Centre for Molecular Plant Breeding, Adelaide http://www.waite.adelaide.edu.au/CRCMPB

- "Winter Wheat Gets New Resistance to Hessian Fly", ARS Press Release http://www.ars.usda.gov/is/pr/hessian0897.htm

- INRA Maize Genome Database http://moulon.moulon.inra.fr/imgd/

- Structural similarity of endochitinase from barley and lysozyme Example from "Dali", a search server for protein 3D structure homologies http://croma.ebi.ac.uk/dali/dali_ex2.html

- EcoCyc, a database of bacterial genes and biochemical pathways http://ecocyc.PangeaSystems.com/ecocyc/ecocyc.html

GrainGenes Database

- Wheat Cultivar Abbreviations update, from Bent Skovmand via AWN 43 500 additional wheat, triticale and barley lines

- 16 barley cDNA clones, mainly pathogenesis-related, from David Collinge Query "find probe data_source = collinge*"

- Photos of 57 Colleagues at the ITMI 1997 Workshop, from Odile Bernard and Dave Matthews "find image *itmi97*"

Quick Queries

- "Sequenced genes" Sequence records for cloned genes. (Not all Sequence records are linked to the corresponding Gene records yet. We're working on it.)

Gopher

- Wheat performance evaluations - Western Regional Performance Nursery Program, from Jim Anderson NEW!

- Annual Wheat Newsletter - Volume 43, 1997, from Jon Raupp For downloading to your own word processor. The online-searchable version is in progress.

- Grains files to browse - Cereal Rust Bulletin - 1997 CRB #7 June 18, #8 July 9, #9 July 22, Final

- Grains files to download - xlloc897.xls The NABGMP clone collection, as an Excel file. From Andy Kleinhofs and Dave Kudrna

Other sources of interesting information

- Barley Genetics Newletter Volume 26: Special Volume, Barley Genetic Stocks Volume 27 Volume 28: In progress. Why wait till '98 to see, or publish, today's data?

- Defence-related cDNA clones from Department of Plant Biology, K.V.L David Collinge's clone collection, mainly barley

- Cornell Small Grains Breeding and Genetics

- Univ of ID Aberdeen 1996 Small Grains Report for SC & SE Idaho

- 1997 Michigan State University Soft Winter Wheat Variety Trials

- Clemson University BAC Center

- Wheat OnLine! Interactive Harvest, Wheat Mania!, Flour Power, and more. A very rich site.

- National Association of Wheat Growers

- American Institute of Baking

- American Malting Barley Association, Inc.

- The Brewery A resource for home brewers.

- Newton's Apple: "What Makes Bread Rise?"

GrainGenes Database

- New Feedback feature! Each record in the database now has a link "Submit comment/correction". Just click there to send us any updates, corrections, complaints, etc.

- Ten microsatellites mapped in wheat Synthetic x Opata, from Mark Sorrells Query "find locus xcnl* microsatellite AND map"

- Waxy protein (starch synthase) genotypes, from Bob Graybosch Alleles for 300 Germplasm lines. Query "find allele wx*".

- Colleague data for 46 members of the ausgrains mailgroup, from Angelo Karakousis

GrainGenes Webserver

- AFLP profiles for 10 additional primer combinations, from Xiaoquan Qi Now 16 barley lines x 34 primer combinations.

Gopher

- Grains files to browse

- Cereal Rust Bulletin

- 1997 CRB #5 May 21, #6 June 4

Other sources of interesting information

- BarleyDB, from SCRI and UK CropNet

- Hog's Head Beer Cellars, Microbrewery beer-of-month club Apologies for mentioning a strictly consumer site, no USDA endorsement implied. But these beers are great examples of the art of H. vulgare! (Please DON'T tell them I sent you, it would be unethical for me to accept their referral special. If you want to express gratitude, send data!)

GrainGenes Database

- 23 new 2_Point_Data records (markers for useful genes), from Greg Penner Query "find 2_point_data trait_marker".

- Lr genes mapped in Synthetic x Opata, from Clare Nelson Trait_Study "Leaf rust, Nelson97"

- Sequences of 1800 Operon and UBC RAPD primers. Probes "Operon*" and "UBC*"

GrainGenes Reports

- "Trait markers" A specific query for Greg Penner's 2_Point_Data records.

- "Microsatellites" SSR primers and corresponding mapped loci.

GrainGenes Gopher

- Wheat quality evaluations

- Hard winter wheat regional quality reports, maintained by Brad Seabourn

- Crop Year 1996, files in text and Excel format

- Grains files to browse:
Cereal Rust Bulletin: 1997 CRB #1 March 25, #2 April 8, #3 April 22, #4 May 6

GrainGenes Webserver

Germplasm

- Molecular Polymorphisms from Zurich 81 European wheat and spelt lines probed with 58 wheat and barley cDNAs. from Monika Messmer, Beat Keller et al.

Other sources of interesting information

- Hard Winter Wheat Regional Nursery Program Upgraded and updated from its previous version on the GrainGenes Gopher.

- Wheat and Small Grains Information, from Missouri Agronomy Extension

- SINGER, System-wide Genetic Resources Programme, from the CGIAR Germplasm characterization data from the International Centers

GrainGenes Database

- 38 SSRs mapped in barley, from M. Saghai Maroof

Query "find probe hvm*".

- 15 SSR primers based on cloned barley genes, from Manfred Heun

"find probe hv*" will find these, plus a few other interesting items.

- Rye map, from Yolanda Loarce

Map_Data "Rye, ExR"

GrainGenes Webserver

- Microsatellite polymorphism in a sample of barley germplasm, from John Korte and Pat Hayes

- Uniform Early and Midseason Oat Performance Nurseries, from Richard Halstead

- Barley Newsletter, Volume 39, 1995, from Rich Horsley

GrainGenes Gopher

- Maps and mapping data

• - Secale
  • - Rye E x R map
  • - Rye E x R mapping data

Tabular versions of the map mentioned above.

- Grains files to browse

- Reserved Laboratory Designators for DNA Clones, Primers and Markers Update from Gary Hart. New designators: ggo, pkg, csu, fdp, labc, rz, ucd, whe, utv, zens.

- Wheat performance evaluations

- HRSW Regional Performance Nursery Program

- Uniform Regional Hard Red Spring Wheat Nursery

- 1996, from Jochum Wiersma

Other sources of interesting data

- The Oregon Wolfe Barleys A collaborative tool for genetics instruction and research using barley as a model system.

- CIMMYTDB, the wheat international nursery database, updated.

- Small Grain Production. Ohio Agronomy Guide, Bulletin 472 Mainly wheat, also oats, barley, triticale, rye.

- 1996 Kentucky Small Grain Variety Trials (wheat and barley) Thanks to Dave Van Sanford for this pointer. (PDF format, requires Acrobat)

- International Grass Genome Initiative (IGGI), from Jeff Bennetzen

- Mugi links. Information on wheat, barley and relatives, in Japanese

- The Korea Rice Genome Database

- The Vavilov Institute of Plant Industry (VIR)

GrainGenes Database

- Rye map, from Perry Gustafson Map_Data "Rye, UC90 x E-line".

- A dozen new primer pairs from Luther Talbert and Nancy Blake. See Probes MWG60, MWG68, WIR1A, WCS66, PGK, PETF, GIRP, EC, CHI, CATHB, AMYA, ACC.

GrainGenes Webserver

-The Dicktoo x Morex Barley Mapping Population, from Pat Hayes Maps, mapping and phenotype data, and QTL analysis.

-Quick Queries: Probes mapped to a specified chromosome

GrainGenes Gopher

- Wheat quality evaluations

- Molecular and genetic data

- Compendium of wheat lines carrying rye chromosome arm 1RS Updated with 150 new lines from the 1996 nurseries, from Bob Graybosch

Other sources of interesting data

-INTERDROUGHT web server, dedicated to promote communication between researchers working on drought tolerance in higher plants. Thanks to Eric Belhassen for notifying us of this site.

-The 1996 Kentucky Small Grain Variety Trials are now available as a downloadable .pdf file (requires Adobe Acrobat Reader).

WEBSERVER NEWS

Some new enhancements to the GrainGenes Web Server have been added:

Probe Repository: A probe repository has been set up at the USDA ARS Western Regional Research Center to provide cereal researchers with a collection of DNA probes to use in their research. The service is free. To date, the probe sources have origins in wheat, oat, and barley genomes. Further information about probes included within the repository is also indexed within the GrainGenes genome database. Send your requests to probes@pw.usda.gov after checking out the site.

Data Forms: GrainGenes is always in the need for new information. If by perusing the GrainGenes Database you find that there is some information missing, incorrect, or needs to be updated, you now have a quick way to get in touch with the curators. Just follow the link from the GrainGenes homepage to the data input forms. You can add information on Colleagues, Research, Metabolic Pathways, Literature, or Comments. If your name is not in the GrainGenes Database, go to the Colleagues Data Form now!

Employment Opportunities: Many times people send job announcements to the grains@greengenes.cit.cornell.edu mailing list. For those people not on the mailing list, they now can be informed by following the link from the GrainGenes homepage to Employment Opportunities.

Meeting Schedules: Likewise, meeting announcements sent to the grains@greengenes.cit.cornell.edu mailing list will be posted. Where possible, links will be made to the meeting web site to find further information.

As always, if there is something missing from the GrainGenes site that you would like to see, please send us a note and we'll try to include it.

DATABASE NEWS

MacGrainGenes on CD-ROM: The GrainGenes Database, running under the Macintosh version of its native ACEDB software, is now available on CD-ROM, along with the Macintosh version of RiceGenes, RiceMac. Contact Dr. Biek Hie Nahm, Myongji University, Yongin, Korea, bhnahm@bioserver.myongji.ac.kr.

For those with Internet access, MacGrainGenes can also still be downloaded from our ftp sites, ftp://probe.nalusda.gov/pub/graingenes and ftp://grain.jouy.inra.fr/pub/database.