Triticeae Genomics

  • Wheat Transcriptome Sequences
    Genome-specific transcriptome sequence datasets to BLAST against.
  • Wheat D Genome Markers
    Genetic map, sequences, and annotation of markers used to anchor the physical map below.
  • WheatDB: Physical Mapping of the Wheat D Genome
    BAC fingerprint contigs and anchoring markers from Aegilops tauschii.
  • 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

EST Projects

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