for the Cotton Community An Online Resource for the Cotton Community Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Katheryn Buble, Ping Zheng, Jodi L. Humann, Deah McGaughey, Heidi Hough, B. Todd Campbell, Richard G. Percy, Don C. Jones, Dorrie Main

CottonGen Introduction Is an online genomics, genetics and breeding (GGB) database, developed in Tripal to help facilitate basic, translational and applied research in cotton It integrates curated publicly available GGB data into a single portal with a suite of querying and analysis tools

Transcripts/RefTrans CottonGen Data Genomes 7 (A2, D5, AD1, AD2) Genes/mRNAs 258,459/503,017 Transcripts/RefTrans 5.8 billion/214,180 Genetic Maps/QTLs 103/1,861 Markers 549,147 Genotypes 391,882 (+21,803,605) Phenotypes 486,310 Germplasm/Images 16,636/12,337 Publications 16,784 CottonGen has the standard types of data you get in a GGB database. In the last year we added RefTrans which combines peer-reviewed published RNA-Seq and EST data sets to create a Reference Transcriptome (RefTrans) for individual Gossypium species and provides putative gene function identified by homology to known proteins.

CottonGen Tools BLAST Map Viewers Genome Browsers CottonCyc Proteins, Genes, Markers, Transcriptoms, Genomes, Map Viewers All Maps Genome Browsers All Genome Assemblies CottonCyc D5 & AD1 Synteny Browser D5 vs A2 Sequence Retrieval All Genome Assemblies and RefTrans Cotton Trait Ontology A central location with controlled vocabulary for cotton phenotypic traits CottonGen BIMS For breeders to store, manage, archive and analyze their private breeding data

http://www.cottongen.org

Species Dropdown - Links to Species Data and Tools

Data Dropdown - Cotton Trait Ontology

Search - Genes and Transcripts

Search – QTL

Search - Germplasm

Tools These are examples of: browsing and searching the Cotton Genes Metabolic Pathways Database AND Browsing conserved syntenic regions between G. arboreum (A2) BGI and G. raimondii (D5) JGI by using Gbrowse_syn

Tools - MapViewer MapViewer will eventually replace CMap on CottonGen Similar to CMap, but uses the Chado data already in database Access MapViewer from “Tools” menu or any genetic map details page MapViewer is a web based genetic map visualization tool that uses the D3 Javascript technology. It allows viewing of genetic maps and will show comparison of genetic maps that share the same markers, across the same or different species. It is similar in functionality to the existing CMap but offers the benefit of using map data directly stored in Chado, a generic database schema.

Tools - Breeding Information Management System All data loaded from a collaborator Breeding Program FieldBook App being used to collect phenotypic data Tools implemented to allow breeder and staff to upload, edit and perform basic data analysis Compare trait data between private and publically available germplasm Currently being tested by breeder

BIMS Home These next too slides just gives you an idea of what BIMS looks like for cotton Login from CottonGen home page accesses the breeders private BIMS

Manage Breeding – Manage Trials Clicking on a trial provides data selectable by trait, stats about the trait and access to view/ download all the data for the trial.

Funding and Acknowledgements It is funded by a partnership between cotton industry and federal support The Cotton Community & The Bioinformatics Community

CottonGen at PAG CottonGen Demo - #C06 CottonGen Poster - #P0599 Tripal Map Poster - #P0091 AgBioData Outreach Booth #407 Presentation #W1026: Updates on Tripal Mapviewer and the Tripal Breeding Information Management System (BIMS)  - Sunday Jan 14, 4.18 PM, California Room