CottonGen is an online knowledgebase developed by the Mainlab at Washington State University to support cotton genomics, genetics, and breeding research, as well as crop improvement. It brings together searchable information and research tools covering cotton species, genes and transcripts, genomes, sequences, genetic markers, maps, germplasm, genotypes, traits, and publications. Users can explore data on diseases, gene relationships, expression, and quantitative trait loci and genome-wide association studies (QTL/GWAS).

The site also provides resources for breeding research, including phenotype and genotype searches, germplasm management, and tools for comparing maps and retrieving sequences. Additional features include BLAST, genome browsing, a GWAS/QTL catalog, a cotton pathway resource, and tools for viewing expression and synteny. CottonGen supports data submission and curation, and offers documentation, tutorials, newsletters, and community information through the International Cotton Genome Initiative (ICGI).

Its resources are intended to help researchers and breeders find, examine, and reuse cotton data for discovery and crop improvement