1. 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

2. 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

3. 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.

4. 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

6. Species Dropdown - Links to Species Data and Tools

7. Data Dropdown - Cotton Trait Ontology

9. Search - Genes and Transcripts

12. Search – QTL

13. Search - Germplasm

14. 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

15. 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.

17. 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

18. 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

19. 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.

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

21. 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