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Triticeae Genomics
Genomics
Marker Development and Cooperative Projects
- 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
- 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:
- 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
- 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
- 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")
Comparative Mapping and Genomics
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