Genomics

• WheatDB phase I
  NSF project "Assessment of the Insular Organization of the Wheat D Genome by Physical Mapping"

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

• PLEXdb
  A USDA-funded public repository for microarray gene expression data. This resource contains information on experiment descriptions, array design, analysis and provides users with the capability to search the contents of the arrays 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.

• Barley SNP Database
  SNPs discovered in the EST contigs used for the Affymetrix Barley1 GeneChip. Includes map positions and genotypes of the mapping parents.

• 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

Marker Development and Cooperative Projects

• TriticeaeGenome
  Genomics for Triticeae improvement. A European project launched in June 2008 for a four-year period, mobilizing 14 European research institutes and 2 industrial partners, from 9 different countries.

• COST Action Tritigen
  Triticeae genomics for the advancement of essential European crops. To coordinate, focus and strengthen national and pan-European Triticeae genomics and to address infrastructure disparities.

• European Triticeae Genomics Initiative (ETGI)
  ETGI coordinates European efforts in barley and wheat physical mapping, sequencing, high resolution genetic mapping, and development of populations for trait mapping with QTLs and association genetics.

• Genoplante / INRA Wheat SSR Club
  This site coordinates the 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.

Genome Sequencing

• INRA TriAnnot Project
  Triticum annotation. Database, BAC annotation pipeline, GBrowse viewer for annotated BACs.

• TIGR's Wheat Genome Database
  A resource for annotated wheat genomic sequence data and comparisons with the rice genome sequence.

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

• International Wheat Genome Sequencing Consortium (IWGSC)
  To facilitate and coordinate international efforts toward obtaining the complete sequence of the hexaploid wheat genome.

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 (CR_EST)
  As of May 2006, this database contains 207,000 ESTs with 1,800,000 corresponding BlastX results and 40,000 consensus sequences. 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.

• 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)
    

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