Marker Development and Cooperative Projects

• Genoplante / INRA Wheat SSR Club
  This site coordinates to effort to characterize simple sequence repeats (SSRs, aka microsatellites) for deposition into the GrainGenes database.

• International Triticeae Mapping Initiative (ITMI)
  ITMI coordinates international efforts in Triticeae linkage and physical mapping, ESTs and bioinformatics, QTLs, large insert libraries, genetic stocks, functional markers and expression analysis.

• TREP, the Triticeae Repeat Sequence Database
  The TREP database contains annotated repetitive DNA sequences from Triticeae species.

• Triticeae EST-SSR Coordination
  A site to compile and distribute SSR-containing ESTs from the Triticeae.

• Wheat SNP Development
  This site serves the coordination of a project to develop single nucleotide polymorphisms (SNPs) in wheat.

EST Projects

• Clemson University Genomics Institute (CUGI)
  A BAC and EST library development center for genomes of agriculturally and environmentally important plants, animals and microbes. CUGI also serves as a repository and distribution center for BAC and EST library resources (clones, filters and whole libraries). See also the Arizona Genomics Institute (AGI).

• International Triticeae EST Cooperative (ITEC)
  This site supported the effort to sequence 40,000 ESTs from the Triticeae. These became public in July 2000.

• IPK (Gatersleben) Barley EST database (B_EST)
  As of June 2002, this database contained 29,107 ESTs with 243,797 corresponding BlastX2 results as well as 2,345 consensus sequences from clusters. Visit the IPK Plant Genome Resources Center (PGRC) homepage for links to other barley projects.

• Japanese wheat ESTs in the KOMUGI database
  116,000 5' and 3' ESTs from Yasunari Ogihara.

• Sugar Cane EST Genome Project (SUCEST)
  This site supports a state funded project in São Paulo, Brazil with the aim of identifying 50,000 sugarcane genes.

• University of Bristol Wheat EST Database
  User-friendly web site to search via BLAST or keywords among 40,000 ESTs from 40 hexaploid winter wheat EST libraries.

• U.S. Wheat EST Project
  A website to accompany the NSF funded project "The Structure and Function of the Expressed Portion of the Wheat Genomes." The site includes:
  • Curated contig assembly for >75,000 wheat and 7,000 rye ESTs
  • Nucleotide sequence alignments for the contigs
  • All BLASTN and BLASTX hits for each EST and contig
  • Downloadable FASTA files of raw and processed sequences and contigs
  • Tracefiles viewable online individually, available in bulk on request. Click here for an example.
  • BLASTable target datasets

• wEST: The GrainGenes companion database of ESTs
  A server of annotated records and BLAST results from the NSF, ITEC and ARS-sponsored wheat EST projects.

Genomics

• BarleyBase
  A USDA-funded public repository for 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.

• Crop Genome Databases
  
  • Barley Genomics
    Washington State University. Databases on molecular markers, ESTs, maps, mutants and barley BACs.
    
  • BarleyDB
    UK Cropnet. ACEDB database with molecular markers, ESTs, QTL, maps.
    
  • Gramene
    USDA-ARS / NSF. Replaced RiceGenes with information on molecular markers, maps, ontology, comparative mapping among grass species.
    
  • MaizeGDB
    USDA-ARS. A comprehensive information source on the genetics, genomics and molecular biology of maize. It is the successor to MaizeDB and ZmDB.
  • MilletGenes
    UK Cropnet. ACEDB database with molecular markers, ESTs, QTL, maps.
    
  • SorghumDB
    UK Cropnet. ACEDB database with molecular markers, ESTs, QTL, maps.
    
  • PlantGDB - Plant Genome Database
    Annotated species-specific EST databases for all major plants, inter-species query capabilities and web-accessible computational tools.

• Haplotype Polymorphism in Polyploid Wheats and Their Diploid Ancestors
  An NSF-supported project to discover and map wheat SNPs. Provides lists of intron-spanning PCR primers derived from mapped ESTs.

• HarvEST
  A Windows software application developed at UC Riverside that enables searching for differentially expressed ESTs among cDNA libraries.

• Marker Assisted Selection in Wheat (MASwheat)
  Bringing genomics to the wheat field. This site supports the project to transfer developments in wheat genomics and biotechnology to production via the organization of a National Wheat MAS Consortium.

• NCBI UniGene Resources
  An experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. UniGene Sets are available for wheat and barley

• Physical Mapping of the Barley Genome
  Database containing BAC libraries, clone fingerprints, markers and contig maps for Hordeum vulgare.

• Physical Mapping of the Wheat D Genome
  Database containing BAC libraries, clone fingerprints, markers and contig maps for Aegilops tauschii.

• Plant Resourcerer
  TIGR annotation of the probes on the Affymetrix Barley1 GeneChip.

• TIGR Gene Indices
  Integrated data from international EST sequencing and gene research projects with the goal of representing all non-reduntant genes and data on expression patterns, functions and evolutionary relationships. Data includes ESTs clustered into Tentative Consensi, top 5 peptide hits, assignment to plantwide Tentative Ortholog Groups ("TOGA"), gene ontology (GO) annotation and alignment to rice BACs and Arabidopsis chromosomes ("Genome Views")
  
  • Barley Gene Index (HvGI)
    
  • Rye Gene Index (RyeGI)
  • Wheat Gene Index (TaGI)
    

• Triticeae Large Insert Libraries
  Comprehensive list of current collections of wheat, barley and other related BAC libraries with links to collection curators.

Comparative Mapping and Genomics

• Gramene: A Comparative Mapping Resource for Grains
  Gramene is a resource to analyze cross species homology deriving its information from public projects in genomics and EST sequencing, protein analysis, mapping, biochemical pathway interpretation, QTLs and ontology.
  Some Gramene data of particular interest to GrainGenes users:
  Comparative genetic maps
  Location of Triticeae ESTs on the rice genome sequence

  KOMUGI
  KOMUGI is an integrated database of wheat, from the National BioResource Project (NBRP) of Japan. It includes:

  • Catalogue of Gene Symbols for Wheat, 2003
  • Comparative map of rice vs. wheat and barley
  • Composite wheat map

  Plant Genomes Central at NCBI
  Coordination site for large-scale genome and EST sequencing projects and genetic maps. The map viewer feature allows users interoperability in aligning several chromosome maps from different mapping studies. Genetic maps are available for:

  • Triticum aestivum genome view
  • Hordeum vulgare genome view
  • Avena genome view