Germplasm Overview Page Trait Descriptor Standard Images CottonGen: Enabling Cotton Research through Big-Data Analysis and Integration www.cottongen.org Jing Yu1, Sook Jung1, Chun-Huai Cheng1, Taein Lee1, Katheryn Buble1, Ping Zheng1, Jodi L. Humann1, Deah McGaughey1, James Crabb1, Heidi Hough1, B. Todd Campbell2, Don C. Jones3 and Dorrie Main1 Washington State University, Pullman, WA, 2. USDA-ARS, Florence, SC, 3.Cotton Incorporated, Cary, NC Abstract CottonGen (www.cottongen.org) is an online community database resource that integrates publicly available genomic, genetic and breeding data and provides a suite of analysis and visualization tools to enable basic and applied research in cotton. Recent updates to CottonGen include: addition of new genome sequences; genome synteny analysis displayed in a new Synteny Viewer with links to syntenic blocks and orthologs and paralogs; annotated and genome mapped reference transcriptomes distilled from billions of published RNASeq and EST reads; genetic maps displayed in the new MapViewer; QTL data, and additional querying and statistical analysis in the BIMS breeding tools, which provides breeders with a secure portal to manage and analyze their private breeding program data as well as access to public breeding datasets such as the Regional Breeders Testing Network trait data as well as germplasm evaluation data from GRIN, China and Uzbekistan. CottonGen is funded by Cotton Incorporated, USDA-ARS, the cotton industry and USDA NIFA NRSP10. Resources @CottonGen_news Key Features Easy-to-use search interfaces for retrieving data on markers, genes, transcripts, sequences, and traits Syntenic Viewer with nine genome comparisons with ortholog data MapViewer for interactive map viewing of genetic maps BIMS, Breeder Data Management and Analysis System Assembled and annotated reference transcriptome (RefTrans) which is searchable using BLAST PathwayCyc G. raimondii and G. hirsutum genomes Available Data 9 whole genome sequences for 2 diploid and 2 tetraploid cotton 573,381 genetic markers and 109 genetic maps 4,923 QTLs, 12,337 images, and 17,640 germplasm 25,227,605 genotype scores and 383,431 phenotype scores Map Viewer Synteny Viewer Cotton Trait Ontology Germplasm Overview Page CottonCyc Genomes Trait Descriptors CottonGen RefTrans Trait Descriptor Standard Images Acknowledged with Thanks The Cotton Research Community