CottonGen: An Integrated Web-Database for Cotton Genomics, Genetics and Breeding Research

CottonGen is the new cotton database that replaces CottonDB and the Cotton Marker Database (CMD) as a community portal for genomics, genetics and breeding research.  Available at CottonGen are diverse data that support basic, translational and applied cotton research. This includes traits, markers, maps, QTLs, germplasm, pathogens, sequences, phenotypic and genotypic data, and references.  New data and functionality include transcriptome and gene characterization by GO, KEGG, InterPro and BLAST,  marker-trait-locus and breeding data, the publicly available D genome sequence and annotation, as well as enhanced tools for easy querying and visualizing research data.  The database is built using the open-source Tripal database infrastructure developed for other plant databases such as Cacao, Citrus, Rosaceae, Vaccinium, Fagaceae and Cool Season Food Legumes. Future development is highlighted including synteny and pathway tools.