Gramene database

Gramene database provides integrated genomic, genetic, and pathway data for major model and crop plants including Arabidopsis, Brachypodium, rice, maize, sorghum, poplar, and grape to support comparative genomics, trait mapping, and evolutionary analyses.

Key Features:

• Ensembl Genome Browser Integration: Integrates Ensembl genome browser infrastructure for coordinate-based annotation and comparative analysis across plant genomes.
• Extensive Data Sets: Hosts quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies, markers, and sequences datasets integrated with genome browsers and genetic, physical, and bin maps derived from published studies.
• Web Services: Provides Distributed Annotation Server (DAS), BLAST sequence alignment services, and a public MySQL database for programmatic data access.
• Regular Updates: Performs major builds twice a year and issues interim releases to incorporate corrections and important dataset or software updates.

Scientific Applications:

• Genetic Diversity Analysis: Enables analysis of genetic diversity using integrated genotype and germplasm datasets across species.
• Trait Mapping and QTL: Supports quantitative trait loci mapping and comparative trait-locus analyses across genetic and physical maps.
• Metabolic Pathway Analysis: Facilitates annotation and comparative analysis of metabolic pathways.
• Comparative and Evolutionary Genomics: Supports comparative genomics and evolutionary biology studies among grasses and other plant lineages.
• Germplasm and Breeding Research: Supports germplasm characterization and breeding-related analyses by linking genetic, phenotypic, and marker data.

Methodology:

Systematic collection, curation, and integration of genomic and genetic data from diverse sources combined with integration into genome browsers and maps; major biannual builds and interim releases update datasets and software.