What's new in GrainGenes in 2003?

Sequence

• BLAST databases
  BLAST search against mapped wheat ESTs, cereal EST-SSRs, Triticeae repeat sequences, consensus sequences from wheat EST assemblies, and Barley1 GeneChip exemplars. Example.
• Cereal genes and wheat ESTs aligned to the sequence of the rice genome
  Update, Oct 7 -- Now all 12 assembled chromosomes. And now includes the NSF mapped wheat ESTs.
• TREP, the Triticeae Repeat Sequence Database, from Thomas Wicker.
  Including annotation for each repeat element. Release 5, fifty new repeats.
• Mapped wheat ESTs
  Chinese Spring deletion-line maps of thousands of ESTs, from the NSF wheat EST project.
• 5' vs. 3' ESTs from the same cDNA clone.
  Loci mapped by the NSF wheat EST project are named to indicate the 5' EST directly. This table gives the names of the corresponding 3' ESTs.

Microsatellites

• New, Sep 19 185 cfa and cfd SSRs from Pierre Sourdille.
  With map positions in Synthetic x Opata and Courtot x Chinese Spring.
• New, Oct 17 EST-SSRs from Cornell and Kansas State U.
  Ca. 400 primer pairs, with test results, including map positions in wheat and rice where possible.
• New, Oct 24 544 BARC SSRs from Rick Ward.
  Many not previously published.
• New, Nov 21 45 sugarcane SSRs (STMSs) from N.K. Singh and Vivek Dalal.
  
• New, Nov 22 13,000 wheat, barley and rice EST-SSR primer pairs, from Mauricio La Rota.
  Designed with Primer3 and available for testing.

Mapping

• Map_Data "Wheat, SxS, FHB QTL"
  25 loci and 5 QTLs for FHB by single spikelet inoculation.
• Map_Data "Wheat, WxM, FHB QTL"
  68 loci and 6 QTLs for FHB field resistance, single floret injection and DON accumulation.
• Map_Data "Wheat, Synthetic x Opata, BARC"
  1410 loci including 222 BARC microsatellite markers mapping onto the SxO population
• Map_Data "Barley, TxE"
  166 loci mapped onto a population of Tadmor (drought tolerant) x Er/Apm (susceptible)
• Map_Data "T.turgidum, JK x Cham1, 2"
  Durum population to map drought tolerance related markers.
• Map_Data "Oat, KxO, 2003"
  Update of the Kanota x Ogle population with the addition of 607 new markers.
• Linkage_Data 5AL, CS x CS-TDIC DS5A"
  Q gene mapped on 5AL using AFLP and differential mRNA display on Chinese Spring deletion lines.
• Map_Data "Wheat, Physical, Group 5"
  Physical mapping on group 5A deletion lines of Chinese Spring. Regions of synteny to rice chromosomes are noted in the breakpoint_interval records.
• Linkage_Data 5AL, CS q deletions, physical"
  Chromosome 5AL physical map and deletion patterns resulting in the 'q' germplasm set.
• 2_Point_Data for the Q gene from AFLP-based mRNA fingerprinting.
  Links to these are found in the Reference record of Molecular and General Genetics 253:635-641.
• Markers for marker-assisted selection of seven traits in wheat.
  With links to the MASwheat website for additional details. From Marcelo Soria and Jorge Dubcovsky.
• High resolution map of the Vrn1 region -- genetic, physical and sequence.
  0.8 cM, 556 kb, eight genes from T. monococcum chromosome 5AL. From Jorge Dubcovsky.
• Map_Data "Wheat, Physical"
  Chinese Spring deletion-line maps of RFLP markers that have also been placed on recombination-based maps.
• Map_Data "Wheat, Physical, EST"
  Chinese Spring deletion-line maps of thousands of ESTs, from the NSF wheat EST project.
• Map_Data "Barley, AxHs/QTL"
  Advanced backcross QTL analysis using microsatellite markers in Apex x H. spontaneum. Thirteen yield and quality traits in up to six environments. From Klaus Pillen.
• New, Oct 6 16,000 wheat EST loci mapped on Chinese Spring deletion lines. From the US NSF wheat EST project.
  Representing a map of this density is challenging. Here are our best representations:
  • wEST-SQL A queryable table format
  • GBrowser
  • GBrowser, alternate site
  • CMap (experimental)
  • ACEDB

Germplasm

• Uniform Regional Hard Red Spring Wheat Nursery Report 2002.
  Click here for a .pdf version.
• Uniform Regional Scab Nursery 2002.
  Click here for a .pdf version.
• Uniform Early and Midseason Oat Performance Nurseries 2002.

Publications

• Image Gallery of the Oregon Wolfe Barleys
  Images of the inflorescences of dominant and recessive parents and 94 doubled haploid lines.
• Catalogue of Gene Symbols for Wheat: 2003 Supplement
  From R.A. McIntosh, K.M. Devos, J. Dubcovsky, C.F. Morris and W.J. Rogers.
• Phenotypic Associative Microsatellite (SSR) Marker Assisted Selection
  12 traits vs. 72 SSRs in 196 BARI experimental barley lines.
  From L.J. Wright, D.B Cooper, P.M. Hayes, I. Matus, K. Richardson, and J. Von Zitzewits.
• Comparative Map of Wheat and Rice Genomes
  Detailed data from the Genome Research article.
  From M.E. Sorrells et al.
• Annual Wheat Newsletter Volume 49, from Jon Raupp.

Miscellaneous

• Snapshots of 46 Colleagues, from the 10IWGS and IGROW conferences.