(updated on March 9, 2017)
- 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.
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
USDA-ARS / NSF. Replaced RiceGenes with information on molecular markers, maps, ontology, comparative mapping among grass species.
USDA-ARS. A comprehensive information source on the genetics, genomics and molecular biology of maize. It is the successor to MaizeDB and ZmDB.
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.
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
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.
- International Wheat Genome Sequencing Consortium (IWGSC)
To facilitate and coordinate international efforts toward obtaining the complete sequence of the hexaploid wheat genome.
- International Barley Sequencing Consortium (IBSC)
Towards physically mapping and sequencing the barley gene space
- IPK Rye BLAST Server
Progress toward sequencing sequencing and assembly of the rye genome.
- The Oat Genome Project
Sequencing the hexaploid oat genome using diploid references.
- 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.
- Japanese wheat ESTs in the KOMUGI database
116,000 5' and 3' ESTs from Yasunari Ogihara.
- 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:
- 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)
Comparative Mapping and Genomics
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: