Genomics

(updated on August 11, 2017)

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.
  • 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

  • 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.
  • EnsemblPlants
    Genome database for plants with tools for comparative analysis, data mining and visualization.
  • 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.
  • 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.
  • Triticeae EST-SSR Coordination
    A site to compile and distribute SSR-containing ESTs from the Triticeae.
  • Barleymap
    Barleymap was designed to search the position of barley genetic markers on the Barley Physical Map (IBSC) and the POPSEQ map (Mascher et al., 2012). The current version was updated to work with the Morex Genome (released in 2017).

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