What's new in GrainGenes? -- 1996

23 December 1996

GrainGenes Database

*Map_Data "Barley, physical", from Gottfried Kuenzel Translocation breakpoints mapped relative to RFLP loci on 1H, 3H, 5H (updates) and 6H (new). As GIF images.

GrainGenes Webserver

*AFLP profiles of barley cultivars, from Xiaoquan Qi 16 cultivars x 24 primer combinations.

Other sources of interesting data

*Institut fuer Pflanzengenetik und Kulturpflanzenforschung, Gatersleben

*Department of Plant Breeding, Wageningen Agricultural University

*COST 817: Airborne pathogens of cereals

*ASA / CSSA / SSSA (American Society of Agronomy et al.)

HAPPY HOLIDAYS, EVERYONE!

- Dave

GrainGenes Release 1.7 available

A new release of GrainGenes (Unix and Macintosh versions) is now available for downloading via anonymous ftp from probe.nalusda.gov:pub/graingenes or grain.jouy.inra.fr:pub/database. Please send inquiries about problems obtaining or installing the database to matthews@greengenes.cit.cornell.edu

New data added since the previous release (April 1996) include:

* 7-chromosome map of barley morphological genes, from Jerry Franckowiak

* Barley Chebec x Harrington, Clipper x Sahara, and Galleon x Haruna nijo maps, from Angelo Karakousis and Peter Langridge

* Update of the barley Igri x Franka map, from Andreas Graner

* Barley Igri x Triumph map, with flowering-time QTLs, from Dave Laurie

* Triticum monococcum map, from Jorge Dubcovsky

* Barley chromosome 5 (1H) gene map update, from Jens Jensen

* 300 T. timopheevii ssp. armeniacum accessions, from Jon Raupp

* Secale cereale map, from Katrien Devos

* 48 photos of Triticeae chromosome banding patterns, from Bernd Friebe

* End sequences and PCR primers for 6 MWG probes, from Takao Komatsuda

* A tan spot QTL in the Synthetic x Opata population, from Justin Faris

* Snapshots of 44 Colleagues at the Saskatoon Oat/Barley Congress.

* Triticum turgidum 6A and 6B maps, from Chen et al., TAG 89:703, 1994

* Passport data for 1400 BCD and CDO probes, from Mark Sorrells

* Trait data for 70 oat lines, from Mark Sorrells

* Integrated barley map, from Xiaoquan Qi

* Barley Vogelsanger Gold x Tystofte Prentice map, from Henriette Giese

* Oat Kanota x Ogle QTL map, from Mark Sorrells

* Chromosome 1R.1D recombinant translocation map, from Peter Langridge

* 240 cloned barley genes, from Penny von Wettstein-Knowles

* Descriptions of 160 NABGMP clones, from Andy Kleinhofs

* 2200 wheat aneuploid and substitution lines, from Perry Gustafson.

* Integrated barley map, from Peter Langridge

* Barley translocations mapped vs. RFLP loci and chromosome bands, from Gottfried Kuenzel

* Oat gene catalog, from Marshall and Shaner 1992, and Simons et al. 1978

* Wheat group 6 map, from Gary Hart and Clare Nelson

* Triticeae consensus map for group 6, from Gary Hart and Clare Nelson

* 151 FBA and FBB probes, from Philippe Leroy

* Barley Steptoe x Morex basemap, from Diane Mather

* Barley Harrington x TR306 basemap, from Diane Mather

--
23 November 1996

LOTS of new data in GrainGenes this month!

GrainGenes Database

Seven-chromosome map of barley morphological genes, from Jerry Franckowiak

Three barley maps from Angelo Karakousis and Peter Langridge

-Chebec x Harrington

-Clipper x Sahara

-Galleon x Haruna nijo

Update of the barley Igri x Franka map, from Andreas Graner

Barley Igri x Triumph map (IxT/QTL), with flowering-time QTLs, from Dave Laurie

Triticum monococcum map (DV92 x G3116), from Jorge Dubcovsky

XNor regions of group 1 and 5 chromosomes, from Jorge Dubcovsky

Quick Queries

"Resistant germplasm"

Accessions rated as "Resistant" or "Immune" or "Low sporulation" from the Wheat Genetics Resource Center.

"Barley genes"

Now contains the genes from the Franckowiak map too.

GrainGenes Gopher

Maps and mapping data (text versions of the maps mentioned above)

Hordeum

-"Barley gene map, 7-chromosome"

-"Barley Chebec x Harrington map"

-"Barley Chebec x Harrington mapping data"

-"Barley Clipper x Sahara map"

-"Barley Clipper x Sahara mapping data"

-"Barley Galleon x Haruna nijo map"

-"Barley Galleon x Haruna nijo mapping data"

-"Barley Igri x Franka map"

-"Barley Igri x Franka mapping data"

-"Barley Igri x Triumph flowering-time map"

Triticum

-"Triticum monococcum DV92 x G3116 map"

-"Triticum monococcum DV92 x G3116 mapping data"

-"XNor regions of group 1 and 5 chromosomes"

GrainGenes Webserver

QTL analysis of barley, from Angelo Karakousis and Peter Langridge

-Chebec x Harrington

-Clipper x Sahara

-Galleon x Haruna nijo

Upcoming meetings of interest to GrainGenes enthusiasts

Welcome Gerry Lazo!!

Gerry is occupant of the new USDA-ARS Geneticist position in the GrainGenes project. He comes to us from the CottonDB project, and has extensive experience in plant genetics and molecular biology. For more details see his WWW home page at http://wheat.pw.usda.gov/homepage/lazo/.

GrainGenes Database

Barley chromosome 5 (1H) gene map update, from Jens Jensen Many molecular markers added. Map_Data "Barley genes".

300 T. timopheevii ssp. armeniacum accessions, from Jon Raupp Evaluated for eight disease and pest resistances. Query "find germplasm *timopheevii*".

Quick Queries

"Nearby Loci" Lists all loci within a specified distance on any map of a given locus.

Sequence records are now directly linked to BLAST (WWW interface only). See Sequence D12921 for example.

Gopher

15. Maps and mapping data

Hordeum

"Barley gene map" updated with the new 5 (1H) map mentioned above.

"Barley gene map images" Gif images of the gene maps for 1H, 2H, and 4H.

World Wide Web

RFLP survey of wheat, from Angelo Karakousis 124 wheat lines x 1969 RFLP bands.

RFLP survey of barley, from Angelo Karakousis 96 barley lines x 1443 RFLP bands.

Other sources of interesting data

MilletGenes, an excellent pearl millet database at the John Innes Centre

SINGER, CGIAR's System-wide Information Network for Genetic Resources

9th International Wheat Genetics Symposium, August 1998

GrainGenes Database

Secale cereale map, from Katrien Devos
"find Map_Data "Rye, Ds2 x RxL10" ".

48 photos of Triticeae chromosome banding patterns, from Bernd Friebe
"find image author = friebe*".

PCR primers for 5 MWG probes and end sequences for 6, from Takao Komatsuda
"find sequence data_source = komatsuda*".

A tan spot QTL in the Synthetic x Opata population, from Justin Faris
"find Trait_Study "Tan spot, Faris95" ".

Data on 32 new barley loci, including 10 telomeres, from Andy Kleinhofs
Probe, mapping enzyme or PCR primers, and chromosome arm location.
"find probe data_source = kleinhofs* AND NEXT = 96.08"

Snapshots of 44 Colleagues at the Saskatoon Oat/Barley Congress. Sorry I didn't get everybody, and some of these pictures aren't the best. If you don't like yours, or you didn't get included, or you weren't even at the meeting, don't feel bad, just send us a photo! We'll take a quick scan and get it right back to you. You don't even have to say what year it was taken. 8-)

Gopher

7. Wheat performance evaluations

State Performance Tests

Kansas, 1996, from Kraig Roozeboom

9. Catalogue of Gene Symbols for Wheat

The 1995 and 1996 Supplements can now be found in this directory. They are also still included in the downloadable versions of the corresponding volumes of the Annual Wheat Newsletter.

10. Annual Wheat Newsletter, 1991-96

Volume 42, 1996, from Jon Raupp For searching online, or downloading to your own word processor.

15. Maps and mapping data

Secale

Rye Ds2 x RxL10 map Tabular form of the rye map mentioned above.

17. Grains files to download

GRIPI.ZIP, from Michael Mackay The Genetic Resources Information Package for Wheat. Passport and genealogical data on 130,000 of the world's wheats.

World Wide Web

Ken's GRIPserver, http://www.psu.missouri.edu/grip Web access to the GRIP I database mentioned above. Under development; only one of the query methods available in the Windows stand-alone version is running so far. Thanks to Ken Kephart.

The NEW GrainGenes Webserver! Our Webserver has been extensively reorganized to make things easier to find. We hope you like it! Nothing has been intentionally removed, just moved, so if you can't find something that used to be there please let us know.

--
20 Aug 1996

GrainGenes Database

Triticum turgidum 6A and 6B maps, from Chen et al., TAG 89:703, 1994 Map_Data "T.turgidum, durum x dicoccoides".

Passport data for 1400 BCD and CDO probes, from Mark Sorrells

Trait data for 70 oat lines, from Mark Sorrells 14 qualitative and 9 quantitative traits. "find trait_study *souza88".

Gopher

8. Wheat quality evaluations

Molecular and genetic data
Granule-bound starch synthase alleles, from Bob Graybosch
GBSS ("waxy protein") alleles for 300 wheat lines.

16. Maps and mapping data

Triticum

Triticum durum x T. dicoccoides 6A, 6B map
Tabular form of the T. turgidum map mentioned above.

17. Grains files to browse

Cereal Rust Bulletin, from Mark Hughes
1996 Reports #8 and Final.

Other sources of interesting data

Saskatchewan Agriculture and Food / Crops / Cereals
http://www.gov.sk.ca/agfood/crops/cereal.htm

Alberta Agriculture, Food and Rural Development / Crops
http://www.agric.gov.ab.ca/crops

Nordic Gene Bank
http://www.ngb.se

A mirror site for CIMMYT
http://www.cgiar.org/cimmyt

18 July 1996

GrainGenes Database

Barley Vogelsanger Gold x Tystofte Prentice map, from Henriette Giese 85 markers. Map_Data "Barley, VGxTP"

Oat Kanota x Ogle QTL map, from Mark Sorrells 7 traits, over 200 QTLs. Map_Data "Oat, KxO/QTL".

Chromosome 1R.1D recombinant translocation map, from Peter Langridge Ten recombinant segments mapped with 55 markers. Map_Data "Wheat.Rye recombinant".

240 cloned barley genes, from Penny von Wettstein-Knowles Query 'find probe information_source = xgm-93-6.110'.

Descriptions of 160 clones, including 50 known-function probes, mapped in the NABGMP barley populations, from Andy Kleinhofs. More to come!

2200 wheat aneuploid and substitution lines, from Perry Gustafson. Query 'find germplasm data_source = gustafson*'.

Gopher

8. Wheat quality evaluations

The Quality menu has been completely reorganized to make it more digestible. Thanks to Brad Seabourn and Scott Haley!

Hard winter wheat regional quality reports This directory is now being maintained directly by Brad Seabourn.

'Crop Year 1995', from Brad Seabourn

Hard red spring wheat quality data

'1995', from Gary Hareland

Durum quality data

'1995', from Gary Hareland

16. Maps and mapping data

Hordeum

"Barley consensus map, Wageningen" Tabular form of the Qi et al. integrated map mentioned above.

"Barley Vogelsanger Gold x Tystofte Prentice map" Tabular form of the VG x TP map mentioned above.

"Barley chromosome numbering reference card" By request.

17. Grains files to browse

"Cereal Rust Bulletin", from Mark Hughes

1996 Reports #6 and #7.

I'm looking forward to seeing many of you in Saskatoon real soon!

- Dave

--

18 June 1996

** Announcing a new server for European GrainGenes users! **

GrainGenes now has a mirror site in Jouy-en-Josas, France, courtesy of INRA and FTMI, through the efforts of Philippe Leroy. This site maintains daily updated copies of all GrainGenes services:

1. GrainGenes Database
   1. gateway for browsing and querying via WWW
   2. anonymous ftp archive for downloading
   3. GrainGenes Webserver
   4. GrainGenes Gopher
   The URL for all these services is http://grain.jouy.inra.fr. We hope this mirror site will greatly enhance the speed and convenience of GrainGenes access from Europe.
   GrainGenes Database

   Map_Data "Barley consensus", from Peter Langridge
   JoinMap synthesis of three published maps and four new ones, 587 markers.

   Map_Data "Barley genes",from Barley Genetics Newsletter 25
   Updates of the 1H and 4H gene maps.

   Map_Data "Barley physical", from Kuenzel et al., BGN 24 and 25.
   106 translocation breakpoints mapped relative to RFLP loci on 1H, 3H, 5H. Look at Maps "Hordeum-Physical-RFLP-*"

   Oat gene catalog, from Marshall and Shaner 1992, and Simons et al. 1978
   Descriptions, synonyms and references for over 300 genes. Query "find gene *avena*".

   Gopher

   17. Wheat quality evaluations

   Please note that the entire directory structure for 'Wheat quality evaluations' has been rearranged. Please take a look!

   16. Maps and mapping data

   Avena

   "Kanota x Ogle oat QTL dataset"
   Data for Siripoonwiwat et al., Journal of Quantitative Trait Loci, 1996 (http://probe.nalusda.gov:8000/otherdocs/jqtl).

   Hordeum

   "Barley consensus map"
   Tabular summary and downloadable images of the Langridge map.

   "Barley gene map"
   Tabular version of the updated 1H and 4H gene maps.

   17. Grains files to browse

   "Cereal Rust Bulletin", from Mark Hughes
   1996 Reports #4 and #5.

23 May 1996

GrainGenes Database

Map_Data "Wheat, Synthetic x Opata": maps for group 6, from Gary Hart and Clare Nelson. With mapping data. All 21 chromosomes are not included. This map was previously named "Wheat, Sorrells". It has been renamed to reflect the collaborative nature of this project.)

151 FBA and FBB probes, from Philippe Leroy. All the facts from "Le Catalogue des Clones Genoble", including autoradiograms and drawings of bands mapped in "Wheat, Synthetic x Opata".

Map_Data "Triticeae consensus" for group 6, from Gary Hart and Clare Nelson. Added to the previous consensus maps for groups 1-3.

Map_Data "Barley, SxM basemap", from Diane Mather. A subset of the Steptoe x Morex map suitable for QTL mapping.

Map_Data "Barley, HxT basemap", from Diane Mather. A subset of the Harrington x TR306 map suitable for QTL mapping.

Map_Data "Barley, Physical", from Marthe and Kuenzel, TAG 89:240,1994. 122 translocation breakpoints mapped relative to chromosome bands.

Germplasm"T*(barley)", from Kuenzel, BGN 22:80, 1992. 415 single translocation stocks in the IPK collection, Gatersleben.

Gopher

16. Maps and mapping data

Triticum

"Wheat W7984 x Opata85 map". Now includes the tabular form of the group 6 maps too.

"Wheat W7984 x Opata85 group 6 mapping data".

17. Grains files to browse

"Cereal Rust Bulletin", from Mark Hughes. 1996 Reports #2 and #3.

"Codon usage tables", from Mike Cherry. codon frequencies in gene sequences from several grass species.

19. Software for genetics

qGene, from Clare Nelson. A Macintosh program for marker-based genetic analysis.

World Wide Web

"The Steptoe x Morex Barley Mapping Population", from Pat Hayes and Memo Briceno. Trait data, mapping data, and QTL results.

"Autoradiogram Images, Kanota x Ogle". Images from the Database, directly hot-linked to a list of loci in map order.

"Autoradiogram Images I, Synthetic W7984 x Opata M85" and "Autoradiogram Images II, Synthetic W7984 x Opata M85". Same for the wheat map (groups 1-3 and 4-7 respectively). This has been available for some months; what's new are the group 6 map and Xfba and Xfbb markers.

"AGIS: Database: GrainGenes", the WWW-accessible copy of the GrainGenes Database, is now being updated daily from the master copy at Cornell U.

http://probe.nalusda.gov:8300/cgi-bin/browse/graingenes.

Other sources of interesting data

CIMMYT

http://www.cimmyt.mx

The Wheat Page at Kansas State University. Status change from "under construction" to "operational". New URL: http://www.ksu.edu/wheatpage

13 April 1996

GrainGenes Database

Proctor x Nudinka map update, "Barley, PxN", from Manfred Heun 118 AFLP and 5 microsatellite markers added. With AFLP autoradiogram.

Wheat Gene Catalogue update, from Gary Hart GrainGenes now contains the entire contents of the 1993 "Catalogue of Gene Symbols for Wheat", plus the DNA Markers from the 1995 Supplement.

Insert sizes for 120 sugarcane CDS probes, from Jorge da Silva

2700 Genbank sequence records From a query for Aegilops, Avena, Hordeum, Saccharum, Secale, or Triticum

Gopher

16. Maps and mapping data

Hordeum

Barley Proctor x Nudinka AFLP,RFLP map Tabular form of the updated map mentioned above.

Barley Proctor x Nudinka AFLP autoradiogram
Image of the survey of 16 primer combinations used in this map, with the 118 mapped bands marked.

World Wide Web

"Quick Queries", http://greengenes.cit.cornell.edu/ggtabledefs.html

"Mapped sequences" A query for all Probes that have both Locus and Sequence data.

Other sources of interesting data

Minnesota Association of Wheat Growers http://www.rrtrade.org/smallgrains

Cereal Rust Laboratory www.umn.edu/rustlab

The Wheat Page at Kansas State University (under construction) http://www.ksu.edu/wheatpage

--

12 March 1996

GrainGenes Database

RFLPs linked to oat crown rust resistance, from Arla Bush Look in class "Linkage_Data", a new class for subchromosome-sized maps.

Iowa State diploid oat map, from Rayapati et al., TAG 89:831, 1994 A. strigosa x A. wiestii, with another crown rust resistance locus.

Five dormancy-related clones, from Kay Walker-Simmons Search for Probe pMA*

Links to Colleagues' WWW homepages
Query: "find colleague www_page"

Gopher

7. Wheat performance evaluations

HRSW Regional Performance Nursery Program

Uniform Regional Hard Red Spring Wheat Nursery, from Jochum Wiersma

State Performance Tests

Minnesota, 1995, from Jochum Wiersma

16. Maps and mapping data

Hordeum

Barley Proctor x Nudinka AFLP,RFLP mapping data, from Manfred Heun

Avena

A. strigosa x A. wiestii map
Tabular form of the diploid oat map mentioned above.

World Wide Web

"Outline of the GrainGenes Webserver"
Complete contents of the Webserver on one searchable page. link to old 1996 outline updated to current 1997 outline. to find the older outline, go back to home, click on the old version of GrainGenes and look for the outline there, the second option available. Thank you.

"Outline of the GrainGenes Gopher"
Contents of the Gopher on one searchable page.

Other sources of interesting data

Images of STS primers tested on seven single-chromosome wheat-barley addition lines, by Tom Blake http://hordeum.oscs.montana.edu/PCRgels

Wheat data from Utah, "The Utah Wheat Breeding Home Plots" http://wheat.usu.edu

--

9 February 1996

GrainGenes Database

New address records for 320 colleagues, and many updates from ITMI Everything should be correct now. If you see anything wrong let us know.

Snapshots of 24 colleagues taken at Plant Genome IV, from Dave Matthews ACEDB query: "find colleague image"

Six new PCR primer pairs for HMW glutenin genes, from Renato D'Ovidio
ACEDB query: "find probe glu*"

Gopher

The maps are still there! They've been moved from "Grains files to browse" to a new item on the main menu, "Maps and mapping data". We hope you find the new menu organization easier to use.

7. Wheat performance evaluations

HRSW Regional Performance Nursery Program/Uniform Regional Scab Nursery Results from ND, SD, MN, and Manitoba, 1995, from Jochum Wiersma

8. Wheat quality evaluations

Hard winter wheat regional quality reports 1993 and 1994, from Brad Seabourn

Search regional quality data, 1971-1994 Update of the 1971-1992 summary data, from Brad Seabourn

PNW regional quality data Western Wheat Quality Laboratory data, 1981-1994, from Bob Graybosch

16. Maps and mapping data

Hordeum Barley Harrington x TR306 QTL dataset, from D. Mather and N. Tinker

Or see it on the Web: http://gnome.agrenv.mcgill.ca/nabgmp/htqtl.htm.

Saccharum

CU,CIBR 1995 map and mapping data Tabular form of the map loaded in the Database in November.

Triticum: T. aestivum and T. monococcum 1A and 1A^m^ maps and mapping data Tabular form of the maps loaded in the database last month.

World Wide Web

"Quick Queries", The "PCR primers" and "Colleagues" reports are updated with the new Database data mentioned above. (Actually these reports are always as current as the Database, automatically updated.)

AE Van Deynze, ME Sorrells and SR McCouch. 1996. Anchor probes for comparative mapping in grass species. http://greengenes.cit.cornell.edu/anchors. Characterization of 153 barley, oat and rice cDNA probes against barley, oat, wheat, rice, maize, sorghum and sugarcane.

Other News

There is now a Web page for NABGMP. No, two of them!!:
NABGMP USA, http://www.css.orst.edu/research/barley/nabgmp.htm
NABGMP Canada, http://gnome.agrenv.mcgill.ca/nabgmp/cnabgmp.htm

Some Web pages of wheat and barley nursery trials:
Missouri 1995, http://www.psu.missouri.edu/pubs/sr478
Kentucky 1995, http://www.uky.edu/Agriculture/Wheat/95testcon.html

--

5 January 1996

GrainGenes Database

21-Chromosome map of wheat genes, from Hart et al., in "Genetic Maps", 1993. Includes 2-point distances; click on a locus, then "Gmap data...".

T. aestivum and T. monococcum 1A and 1A^m^ maps, from Jorge Dubcovsky Updated and extended from the previous (December 1994) versions.

Triticeae consensus map, from Allen Van Deynze and Clare Nelson
Groups 1 - 3 (Database version of Gopher files loaded April 1995).

Catalogue of Gene Symbols for Wheat, DNA Markers section, from Gary Hart All DNA Markers from the 1993 Catalogue and Supplements are now loaded.

Collections of Triticum, Hordeum, Avena, and Saccharum spp., from IPGRI Address information and species held in each of 200 collections.

Descriptions of 40 OG (oat genomic) clones, from Mark Sorrells

Gopher

7. Wheat performance evaluations

State Performance Tests

New York, 1995, from Mark Sorrells

16. Grains files to browse

"Barley gene map", chromosomes 2, 4 and 5, from BGN volume 24 Tabular version of the maps loaded in the Database last month.

"Wheat gene map" Tabular version of the Hart et al. map in the Database (see above).

World Wide Web

Quick Queries, Generate a current report of GrainGenes data on the indicated topics.

Happy 1996 from GrainGenes!! We hope to see you all at Plant Genome IV.

- Dave