Cotton Gen Enabling Cotton Research through BigData Analysis

Cotton. Gen: Enabling Cotton Research through Big-Data Analysis and Integration www. cottongen. org Jing Yu 1, Sook Jung 1, Chun-Huai Cheng 1, Taein Lee 1, Katheryn Buble 1, Ping Zheng 1, Jodi L. Humann 1, Deah Mc. Gaughey 1, James Crabb 1, Heidi Hough 1, B. Todd Campbell 2, Don C. Jones 3 and Dorrie Main 1 1. Washington State University, Pullman, WA, 2. USDA-ARS, Florence, SC, 3. Cotton Incorporated, Cary, NC Abstract Cotton. Gen (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 Cotton. Gen 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 Map. Viewer; 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. Cotton. Gen is funded by Cotton Incorporated, USDA-ARS, the cotton industry and USDA NIFA NRSP 10. Resources Key Features @Cotton. Gen_news • Easy-to-use search interfaces for retrieving data on markers, genes, transcripts, sequences, and traits • Syntenic Viewer with nine genome comparisons with ortholog data • Map. Viewer for interactive map viewing of genetic maps • BIMS, Breeder Data Management and Analysis System • Assembled annotated reference transcriptome (Ref. Trans) which is searchable using BLAST • Pathway. Cyc 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 Cotton Trait Ontology Map Viewer Synteny Viewer Germplasm Overview Page Cotton. Cyc Cotton. Gen Ref. Trans Genomes Trait Descriptor Standard Images Acknowledged with Thanks The Cotton Research Community